[med-svn] [r-bioc-gviz] 01/05: New upstream version 1.20.0
Andreas Tille
tille at debian.org
Fri Sep 22 13:58:32 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-gviz.
commit 283e7b206a2fccce33f11bedb3bf7794407193c8
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 22 15:34:40 2017 +0200
New upstream version 1.20.0
---
DESCRIPTION | 4 +-
NAMESPACE | 6 +
NEWS | 13 +
R/AllClasses.R | 46 +-
R/Gviz-methods.R | 32 +-
R/Gviz.R | 7 +-
Rplots.pdf | Bin 3611 -> 3611 bytes
build/vignette.rds | Bin 225 -> 224 bytes
inst/doc/Gviz.R | 2 +-
inst/doc/Gviz.Rnw | 4 +-
inst/doc/Gviz.pdf | Bin 1454409 -> 1498771 bytes
inst/extdata/biomartVersionsLatest.txt | 2 +-
inst/extdata/biomartVersionsNow.txt | 2 +-
inst/scripts/documentation.R | 2 +
man/AlignedReadTrack-class.Rd | 712 +++++------
man/AlignmentsTrack-class.Rd | 3 +
man/AnnotationTrack-class.Rd | 5 +-
man/BiomartGeneRegionTrack-class.Rd | 400 +++---
man/CustomTrack-class.Rd | 8 +-
man/DataTrack-class.Rd | 230 ++--
man/DisplayPars-class.Rd | 1 +
man/GdObject-class.Rd | 3 +
man/GeneRegionTrack-class.Rd | 5 +-
man/GenomeAxisTrack-class.Rd | 474 ++++----
man/HighlightTrack-class.Rd | 5 +-
man/IdeogramTrack-class.Rd | 120 +-
man/ImageMap-class.Rd | 1 +
man/NumericTrack-class.Rd | 1 +
man/OverlayTrack-class.Rd | 5 +-
man/RangeTrack-class.Rd | 558 ++++-----
man/ReferenceTrack-class.Rd | 1 +
man/SequenceTrack-class.Rd | 11 +-
man/StackedTrack-class.Rd | 600 ++++-----
man/UcscTrack.Rd | 1 +
man/collapsing.Rd | 1 +
man/datasets.Rd | 1 +
man/exportTracks.Rd | 1 +
man/grouping.Rd | 1 +
man/plotTracks.Rd | 1 +
man/settings.Rd | 2089 ++++++++++++++++++++------------
vignettes/Gviz.Rnw | 4 +-
41 files changed, 3051 insertions(+), 2311 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index a941fed..9fa85de 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: Gviz
-Version: 1.18.1
+Version: 1.20.0
Title: Plotting data and annotation information along genomic
coordinates
Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09 at imperial.ac.uk>, Lance Parsons <lparsons at princeton.edu>, Shraddha Pai <shraddha.pai at utoronto.ca>
@@ -20,4 +20,4 @@ Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
License: Artistic-2.0
LazyLoad: yes
NeedsCompilation: no
-Packaged: 2016-11-25 00:05:34 UTC; biocbuild
+Packaged: 2017-04-24 23:15:45 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index dec0033..b9f2642 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -70,6 +70,12 @@ importFrom(utils, assignInNamespace, browseURL, write.table)
importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer, GAlignments, summarizeJunctions)
+importFrom(grDevices, "dev.cur", "dev.off")
+
+importFrom(stats, "setNames")
+
+importFrom(utils, "modifyList", "type.convert")
+
###
export(".chrName",
diff --git a/NEWS b/NEWS
index 9a7655f..8e9fac5 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,16 @@
+CHANGES IN VERSION 1.20.0
+-------------------------
+BUG FIXES
+
+ o BiomartGeneRegionTracks can now deal with a featureMap list to provide
+ alternative conditional mappings for different Biomarts.
+
+CHANGES IN VERSION 1.18.0
+-------------------------
+BUG FIXES
+
+ o Various bug fixes.
+
CHANGES IN VERSION 1.16.0
-------------------------
diff --git a/R/AllClasses.R b/R/AllClasses.R
index a3c23c3..f274f63 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -1008,10 +1008,11 @@ setClass("BiomartGeneRegionTrack",
## Helper to return the default biomart to feature mapping
.getBMFeatureMap <- function(){
- return(c(gene_id="ensembl_gene_id",transcript_id="ensembl_transcript_id", exon_id="ensembl_exon_id",
+ return(list(gene_id="ensembl_gene_id",transcript_id="ensembl_transcript_id", exon_id="ensembl_exon_id",
start="exon_chrom_start", end="exon_chrom_end", rank="rank", strand="strand",
- symbol="external_gene_name", feature="gene_biotype", chromosome="chromosome_name",
- u5s="5_utr_start", u5e="5_utr_end", u3s="3_utr_start", u3e="3_utr_end", cdsl="cds_length", phase="phase"))
+ symbol=c("external_gene_name", "external_gene_id"), feature="gene_biotype", chromosome="chromosome_name",
+ u5s="5_utr_start", u5e="5_utr_end", u3s="3_utr_start", u3e="3_utr_end", cdsl=c("cds_length", "cds_start"),
+ phase="phase"))
}
## Helper to do the actual fetching of data from Biomart
@@ -1021,22 +1022,23 @@ setClass("BiomartGeneRegionTrack",
}
## The map between Biomart DB fields and annotation features. The individual values can be vectors for cases where there is
## ambiguity between different marts. This will be dynamically evaluated against available filters.
- featureMap <- as.list(.dpOrDefault(object, ".__featureMap", list(gene_id="ensembl_gene_id",
- transcript_id="ensembl_transcript_id",
- exon_id="ensembl_exon_id",
- start="exon_chrom_start",
- end="exon_chrom_end",
- rank="rank",
- strand="strand",
- symbol=c("external_gene_name", "external_gene_id"),
- feature="gene_biotype",
- chromosome="chromosome_name",
- u5s="5_utr_start",
- u5e="5_utr_end",
- u3s="3_utr_start",
- u3e="3_utr_end",
- cdsl="cds_length",
- phase="phase")))
+ origFeatureMap <- list(gene_id="ensembl_gene_id",
+ transcript_id="ensembl_transcript_id",
+ exon_id="ensembl_exon_id",
+ start="exon_chrom_start",
+ end="exon_chrom_end",
+ rank="rank",
+ strand="strand",
+ symbol=c("external_gene_name", "external_gene_id"),
+ feature="gene_biotype",
+ chromosome="chromosome_name",
+ u5s="5_utr_start",
+ u5e="5_utr_end",
+ u3s="3_utr_start",
+ u3e="3_utr_end",
+ cdsl=c("cds_length", "cds_start"),
+ phase="phase")
+ featureMap <- modifyList(origFeatureMap, as.list(.dpOrDefault(object, ".__featureMap", list())))
needed <- c("gene_id","transcript_id", "exon_id", "start", "end", "rank", "strand", "symbol", "feature",
"chromosome", "u5s", "u5e", "u3s", "u3e", "cdsl", "phase")
if(!all(needed %in% names(featureMap)))
@@ -1324,7 +1326,7 @@ setMethod("initialize", "GenomeAxisTrack", function(.Object, range, ids, ...){
if(missing(range) || is.null(range))
range <- GRanges()
if(is(range, "IRanges"))
- range <- GRanges(range=range, seqnames="dummy", id=ids)
+ range <- GRanges(ranges=range, seqnames="dummy", id=ids)
.Object at range <- range
.Object<- callNextMethod(.Object, ...)
return(.Object)
@@ -1628,7 +1630,7 @@ setMethod("initialize", "IdeogramTrack", function(.Object, genome, chromosome, b
bnames[sel] <- paste("band", seq_len(sum(sel)), sep="_")
if(any(bnames == ""))
bnames[bnames == ""] <- sprintf("band_%i", which(bnames == ""))
- ranges <- GRanges(seqnames=bnames, range=IRanges(start=bands$chromStart, end=bands$chromEnd),
+ ranges <- GRanges(seqnames=bnames, ranges=IRanges(start=bands$chromStart, end=bands$chromEnd),
name=bnames, type=as.character(bands$gieStain))
.Object <- callNextMethod(.Object=.Object, range=ranges, genome=genome, chromosome=chromosome, name=name, ...)
return(.Object)
@@ -1885,7 +1887,7 @@ setMethod("initialize", "AlignedReadTrack", function(.Object, coverageOnly=FALSE
## to <- max(unlist(lapply(.Object at coverage, function(y) if(length(y)) max(end(y)))))
from <- min(start(range(.Object)))
to <- max(end(range(.Object)))
- .Object at range <- GRanges(range=IRanges(start=from, end=to),
+ .Object at range <- GRanges(ranges=IRanges(start=from, end=to),
strand=names(.Object at coverage), seqnames=.Object at chromosome)
.Object at coverageOnly <- coverageOnly
}
diff --git a/R/Gviz-methods.R b/R/Gviz-methods.R
index e45222e..116833d 100644
--- a/R/Gviz-methods.R
+++ b/R/Gviz-methods.R
@@ -924,7 +924,7 @@ setMethod("collapseTrack", signature(GdObject="DataTrack"), function(GdObject, d
{
sc <- matrix(agFun(sc), ncol=1)
rtmp <- IRanges(start=max(1,drange[1]), end=max(1, drange[2]-1))
- r <- if(is(r, "GRanges")) GRanges(seqnames=seqnames(r)[1], range=rtmp) else rtmp
+ r <- if(is(r, "GRanges")) GRanges(seqnames=seqnames(r)[1], ranges=rtmp) else rtmp
} else if(window<1){
if(is.null(windowSize))
windowSize <- (max(GdObject)-min(GdObject))/100
@@ -965,7 +965,7 @@ setMethod("collapseTrack", signature(GdObject="DataTrack"), function(GdObject, d
scn <- matrix(scn, nrow=nrow(values(GdObject)), dimnames=list(NULL, as.character(unique(ol[,1]))))
sc <- matrix(NA, ncol=length(ir), nrow=nrow(scn))
sc[, as.integer(colnames(scn))] <- scn
- r <- if(is(r, "GRanges")) GRanges(seqnames=chromosome(GdObject), range=ir,
+ r <- if(is(r, "GRanges")) GRanges(seqnames=chromosome(GdObject), ranges=ir,
strand=unique(as.character(strand(GdObject)))) else ir
}
GdObject at range <- r
@@ -1003,7 +1003,7 @@ setMethod("collapseTrack", signature(GdObject="DataTrack"), function(GdObject, d
}
sc <- values(GdObject)
if(length(rr)==1){
- r <- GRanges(seqnames=1, strand=strand(GdObject)[1], range=rr)
+ r <- GRanges(seqnames=1, strand=strand(GdObject)[1], ranges=rr)
GdObject at range <- r
GdObject at data <- matrix(rowMeans(sc, na.rm=TRUE), ncol=1)
} else if(length(rr) < length(r)){
@@ -1024,7 +1024,7 @@ setMethod("collapseTrack", signature(GdObject="DataTrack"), function(GdObject, d
sapply(vsplit, function(x) apply(matrix(x, nrow=nrow(sc), byrow=TRUE), 1, function(y) agFun(y)[1]), USE.NAMES=FALSE)
} else stop("display parameter 'aggregation' has to be a function or a character ", "scalar in c('mean', 'median', 'sum')")
}
- r <- GRanges(seqnames=seq_len(length(rr)), strand=st, range=rr)
+ r <- GRanges(seqnames=seq_len(length(rr)), strand=st, ranges=rr)
GdObject at data <- newScore
GdObject at range <- r
}
@@ -1244,7 +1244,7 @@ setMethod("subset", signature(x="AlignedReadTrack"), function(x, from=NULL, to=N
from <- min(unlist(lapply(x at coverage, function(y) if(length(y)) head(start(y)[runValue(y)!=0],1))))
to <- max(unlist(lapply(x at coverage, function(y) if(length(y)) tail(end(y),2)[1])))
}
- x at range <- GRanges(range=IRanges(start=from, end=to), strand=names(x at coverage), seqnames=x at chromosome)
+ x at range <- GRanges(ranges=IRanges(start=from, end=to), strand=names(x at coverage), seqnames=x at chromosome)
}else{
x <- callNextMethod(x=x, from=from, to=to, sort=sort, stacks=stacks)
}
@@ -2032,9 +2032,23 @@ setMethod("drawGD", signature("AlignmentsTrack"), function(GdObject, minBase, ma
sashFilter <- .dpOrDefault(GdObject, "sashimiFilter", NULL)
sashFilterTolerance <- .dpOrDefault(GdObject, "sashimiFilterTolerance", 0L)
sashNumbers <- .dpOrDefault(GdObject, "sashimiNumbers", FALSE)
- displayPars(GdObject) <- list(".__sashimi"=.sashimi.junctions(ranges(GdObject), score=sashScore,
- lwd.max=sashLwdMax, strand=sashStrand, filter=sashFilter,
- filterTolerance=sashFilterTolerance),
+ sash <- .dpOrDefault(GdObject, "sashimiJunctions", NULL)
+ if (is.null(sash)) {
+ sash <- .create.summarizedJunctions.for.sashimi.junctions(ranges(GdObject))
+ } else {
+ if (class(sash)!="GRanges")
+ stop("\"sashimiJunctions\" object must be of \"GRanges\" class!")
+ sashMcolName <- if (sashStrand=="+") "plus_score" else if (sashStrand=="-") "minus_score" else "score"
+ if (sum(colnames(mcols(sash))==sashMcolName) != 1)
+ stop(sprintf("\"mcols\" of \"sashimiJunctions\" object must contain column named \"%s\",\n which matches the specified (%s) \"sashimiStrand\"!", sashMcolName, sashStrand))
+ }
+ sash <- .convert.summarizedJunctions.to.sashimi.junctions(juns=sash,
+ score=sashScore,
+ lwd.max=sashLwdMax,
+ strand=sashStrand,
+ filter=sashFilter,
+ filterTolerance=sashFilterTolerance)
+ displayPars(GdObject) <- list(".__sashimi"=sash,
".__sashimiHeight"=sashHeight,
".__sashimiSpace"=sashSpace,
".__sashimiNumbers"=sashNumbers)
@@ -4203,7 +4217,7 @@ setMethod(".buildRange", signature("IRanges"),
return(range)
if(missing(chromosome) || is.null(chromosome))
stop("Unable to find chromosome information in any of the arguments")
- range <- GRanges(seqnames=.chrName(chromosome), range=range, strand=if(!is.null(args$strand)) args$strand else "*")
+ range <- GRanges(seqnames=.chrName(chromosome), ranges=range, strand=if(!is.null(args$strand)) args$strand else "*")
if(length(range))
{
vals <- .fillWithDefaults(defaults=defaults, args=args, len=(length(range)), by=NULL, ignore="strand")
diff --git a/R/Gviz.R b/R/Gviz.R
index 686910f..4cbd6d9 100644
--- a/R/Gviz.R
+++ b/R/Gviz.R
@@ -2595,14 +2595,17 @@ availableDefaultMapping <- function(file, trackType){
## Create list for drawing sashimi-like plots
## using summarizeJunctions on GAlignments
## plotting is done via grid.xspline (requires x, y, id, score)
-.sashimi.junctions <- function(range, score=1L, lwd.max=10, strand="*", filter=NULL, filterTolerance=0L) {
- ## summarizeJunctions
+.create.summarizedJunctions.for.sashimi.junctions <- function(range) {
range <- sort(range)
range <- range[!duplicated(range$entityId)]
ga <- GAlignments(seqnames=seqnames(range), pos=start(range), cigar=range$cigar,
strand=if(is.null(range$readStrand)) strand(range) else range$readStrand,
seqlengths=seqlengths(range))
juns <- summarizeJunctions(ga)
+ juns
+}
+
+.convert.summarizedJunctions.to.sashimi.junctions <- function(juns, score=1L, lwd.max=10, strand="*", filter=NULL, filterTolerance=0L) {
## filter junctions
if (!is.null(filter)) {
## if filterTolerance is > 0 than pass it as maxgap parameter in findOverlaps
diff --git a/Rplots.pdf b/Rplots.pdf
index 0ef3db6..d2d4018 100644
Binary files a/Rplots.pdf and b/Rplots.pdf differ
diff --git a/build/vignette.rds b/build/vignette.rds
index 26e244d..11d785e 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/Gviz.R b/inst/doc/Gviz.R
index 4add0ba..a4e937f 100644
--- a/inst/doc/Gviz.R
+++ b/inst/doc/Gviz.R
@@ -809,7 +809,7 @@ library(biomaRt)
bm <- useMart(host="may2012.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl")
fm <- Gviz:::.getBMFeatureMap()
-fm["symbol"] <- "external_gene_id"
+fm[["symbol"]] <- "external_gene_id"
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr7", start=20e6, end=21e6,name="ENSEMBL",
featureMap=fm, biomart=bm)
plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
diff --git a/inst/doc/Gviz.Rnw b/inst/doc/Gviz.Rnw
index f68a9a4..5e68eec 100644
--- a/inst/doc/Gviz.Rnw
+++ b/inst/doc/Gviz.Rnw
@@ -1743,7 +1743,7 @@ library(biomaRt)
bm <- useMart(host="may2012.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl")
fm <- Gviz:::.getBMFeatureMap()
-fm["symbol"] <- "external_gene_id"
+fm[["symbol"]] <- "external_gene_id"
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr7", start=20e6, end=21e6,name="ENSEMBL",
featureMap=fm, biomart=bm)
plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
@@ -2127,7 +2127,7 @@ and read pairs are connected by a bright gray line. Gaps in
the alignments are show by the connecting dark gray lines. Numbers of
reads supporting each gap can be visualized as ``sashimi plot''
\cite{Katz22012015} by adding \Rfunarg{``sashimi''} as an additional
-agument to the \Rfunarg{type} display parameter.
+agument to the \Rfunarg{type} display parameter.
The axis in the title panel shows the relationship between the line
width the the number of reads spanning a given junction. The height of
diff --git a/inst/doc/Gviz.pdf b/inst/doc/Gviz.pdf
index b490aa9..a0fab7d 100644
Binary files a/inst/doc/Gviz.pdf and b/inst/doc/Gviz.pdf differ
diff --git a/inst/extdata/biomartVersionsLatest.txt b/inst/extdata/biomartVersionsLatest.txt
index f72d7cb..8f5dd49 100644
--- a/inst/extdata/biomartVersionsLatest.txt
+++ b/inst/extdata/biomartVersionsLatest.txt
@@ -1 +1 @@
-species dateversion value dataset version date ucscId speciesShort speciesLong
Ailuropoda melanoleuca (Panda) Dec.2014v78 ailMel1 amelanoleuca_gene_ensembl 78 Dec.2014 ailMel1 Panda Ailuropoda melanoleuca
Anas platyrhynchos (Duck) Dec.2014v78 BGI_duck_1.0 aplatyrhynchos_gene_ensembl 78 Dec.2014 anaPlat1 Duck Anas platyrhynchos
Anolis carolinensis (Anole lizard) May.2009v54 AnoCar1.0 acarolinensis_gene_ensembl 54 May.2009 anoCar1 Anole lizard Anolis carolinensis
Anolis carolinensis (Anole lizard) Dec.2014v78 AnoCar2.0 acarolinensis_gene_ensembl 78 Dec.2014 anoCar2 Anole lizard Anolis carolinensis
Astyanax mexicanus (Cave fish) Dec.2014v78 AstMex102 amexicanus_gene_ensembl 78 Dec.2014 astMex1 Cave fish Astyanax mexicanus
Bos taurus (Cow) May.2009v54 Btau_4.0 btaurus_gene_ensembl 54 May.2009 bosTau4 Cow Bos taurus
Bos taurus (Cow) Dec.2014v78 UMD3.1 btaurus_gene_ensembl 78 Dec.2014 bosTau6 Cow Bos taurus
Caenorhabditis elegans May.2009v54 WS190 celegans_gene_ensembl 54 May.2009 ce6 Caenorhabditis elegans Caenorhabditis elegans
Caenorhabditis elegans Aug.2010v59 WS210 celegans_gene_ensembl 59 Aug.2010 ce9 Caenorhabditis elegans Caenorhabditis elegans
Caenorhabditis elegans Oct.2012v69 WBcel215 celegans_gene_ensembl 69 Oct.2012 ce8 Caenorhabditis elegans Caenorhabditis elegans
Caenorhabditis elegans Dec.2014v78 WBcel235 celegans_gene_ensembl 78 Dec.2014 ce10 Caenorhabditis elegans Caenorhabditis elegans
Callithrix jacchus (Marmoset) Dec.2014v78 C_jacchus3.2.1 cjacchus_gene_ensembl 78 Dec.2014 calJac3 Marmoset Callithrix jacchus
Canis familiaris (Dog) May.2012v67 CanFam_2.0 cfamiliaris_gene_ensembl 66 May.2012 canFam2 Dog Canis familiaris
Canis familiaris (Dog) Dec.2014v78 CanFam3.1 cfamiliaris_gene_ensembl 78 Dec.2014 canFam3 Dog Canis familiaris
Cavia porcellus (Guinea Pig) Dec.2014v78 cavPor3 cporcellus_gene_ensembl 78 Dec.2014 cavPor3 Guinea Pig Cavia porcellus
Chlorocebus sabaeus (Vervet-AGM) Dec.2014v78 ChlSab1.1 csabaeus_gene_ensembl 78 Dec.2014 chlSab1 Vervet-AGM Chlorocebus sabaeus
Choloepus hoffmanni (Sloth) Dec.2014v78 choHof1 choffmanni_gene_ensembl 78 Dec.2014 choHof1 Sloth Choloepus hoffmanni
Ciona intestinalis Dec.2014v78 KH cintestinalis_gene_ensembl 78 Dec.2014 ci2 Ciona intestinalis Ciona intestinalis
Ciona savignyi Dec.2014v78 CSAV2.0 csavignyi_gene_ensembl 78 Dec.2014 cioSav2 Ciona savignyi Ciona savignyi
Danio rerio (Zebrafish) May.2009v54 Zv8 drerio_gene_ensembl 54 May.2009 danRer7 Zebrafish Danio rerio
Danio rerio (Zebrafish) Dec.2014v78 Zv9 drerio_gene_ensembl 78 Dec.2014 danRer6 Zebrafish Danio rerio
Dasypus novemcinctus (Armadillo) Dec.2011v65 ARMA dnovemcinctus_gene_ensembl 65 Dec.2011 dasNov3 Armadillo Dasypus novemcinctus
Dasypus novemcinctus (Armadillo) May.2012v67 dasNov2 dnovemcinctus_gene_ensembl 66 May.2012 dasNov2 Armadillo Dasypus novemcinctus
Dasypus novemcinctus (Armadillo) Dec.2014v78 Dasnov3.0 dnovemcinctus_gene_ensembl 78 Dec.2014 dasNov3 Armadillo Dasypus novemcinctus
Dipodomys ordii (Kangaroo rat) Dec.2014v78 dipOrd1 dordii_gene_ensembl 78 Dec.2014 dipOrd1 Kangaroo rat Dipodomys ordii
Drosophila melanogaster (Fly) Dec.2014v78 BDGP5 dmelanogaster_gene_ensembl 78 Dec.2014 dm3 Fly Drosophila melanogaster
Echinops telfairi (Tenrec) Dec.2014v78 TENREC etelfairi_gene_ensembl 78 Dec.2014 echTel2 Tenrec Echinops telfairi
Equus caballus (Horse) Dec.2014v78 EquCab2 ecaballus_gene_ensembl 78 Dec.2014 equCab2 Horse Equus caballus
Erinaceus europaeus (Hedgehog) Dec.2014v78 eriEur1 eeuropaeus_gene_ensembl 78 Dec.2014 eriEur1 Hedgehog Erinaceus europaeus
Felis catus (Cat) Dec.2014v78 Felis_catus_6.2 fcatus_gene_ensembl 78 Dec.2014 felCat5 Cat Felis catus
Ficedula albicollis (Collared flycatcher) Dec.2014v78 FicAlb_1.4 falbicollis_gene_ensembl 78 Dec.2014 ficAlb1 Collared flycatcher Ficedula albicollis
Gadus morhua (Cod) Dec.2014v78 gadMor1 gmorhua_gene_ensembl 78 Dec.2014 gadMor1 Cod Gadus morhua
Gallus gallus (Chicken) May.2012v67 WASHUC2 ggallus_gene_ensembl 66 May.2012 galGal3 Chicken Gallus gallus
Gallus gallus (Chicken) Dec.2014v78 Galgal4 ggallus_gene_ensembl 78 Dec.2014 galGal4 Chicken Gallus gallus
Gasterosteus aculeatus (Stickleback) Dec.2014v78 BROADS1 gaculeatus_gene_ensembl 78 Dec.2014 gasAcu1 Stickleback Gasterosteus aculeatus
Gorilla gorilla (Gorilla) May.2009v54 gorGor1 ggorilla_gene_ensembl 54 May.2009 gorGor1 Gorilla Gorilla gorilla
Gorilla gorilla (Gorilla) Dec.2014v78 gorGor3.1 ggorilla_gene_ensembl 78 Dec.2014 gorGor3 Gorilla Gorilla gorilla
Homo sapiens (Human) May.2009v54 NCBI36 hsapiens_gene_ensembl 54 May.2009 hg18 Human Homo sapiens
Homo sapiens (Human) Feb.2014v75 GRCh37.p13 hsapiens_gene_ensembl 75 Feb.2014 hg19 Human Homo sapiens
Homo sapiens (Human) Dec.2014v78 GRCh38 hsapiens_gene_ensembl 78 Dec.2014 hg38 Human Homo sapiens
Ictidomys tridecemlineatus (Squirrel) May.2009v54 speTri1 stridecemlineatus_gene_ensembl 54 May.2009 speTri1 Squirrel Ictidomys tridecemlineatus
Ictidomys tridecemlineatus (Squirrel) Dec.2014v78 spetri2 itridecemlineatus_gene_ensembl 78 Dec.2014 speTri2 Squirrel Ictidomys tridecemlineatus
Latimeria chalumnae (Coelacanth) Dec.2014v78 LatCha1 lchalumnae_gene_ensembl 78 Dec.2014 latCha1 Coelacanth Latimeria chalumnae
Lepisosteus oculatus (Spotted gar) Dec.2014v78 LepOcu1 loculatus_gene_ensembl 78 Dec.2014 lepOcu1 Spotted gar Lepisosteus oculatus
Loxodonta africana (Elephant) May.2009v54 loxAfr2 lafricana_gene_ensembl 54 May.2009 loxAfr2 Elephant Loxodonta africana
Loxodonta africana (Elephant) Dec.2014v78 Loxafr3.0 lafricana_gene_ensembl 78 Dec.2014 loxAfr3 Elephant Loxodonta africana
Macaca mulatta (Macaque) Dec.2014v78 MMUL1.0 mmulatta_gene_ensembl 78 Dec.2014 mMul1 Macaque Macaca mulatta
Macropus eugenii (Wallaby) Dec.2014v78 Meug_1.0 meugenii_gene_ensembl 78 Dec.2014 macEug2 Wallaby Macropus eugenii
Meleagris gallopavo (Turkey) Dec.2014v78 Turkey_2.01 mgallopavo_gene_ensembl 78 Dec.2014 melGa1 Turkey Meleagris gallopavo
Microcebus murinus (Mouse lemur) Dec.2014v78 micMur1 mmurinus_gene_ensembl 78 Dec.2014 micMur1 Mouse lemur Microcebus murinus
Monodelphis domestica (Opossum) Dec.2014v78 monDom5 mdomestica_gene_ensembl 78 Dec.2014 monDom5 Opossum Monodelphis domestica
Mus musculus (Mouse) May.2012v67 NCBIM37 mmusculus_gene_ensembl 66 May.2012 mm9 Mouse Mus musculus
Mus musculus (Mouse) Dec.2014v78 GRCm38.p3 mmusculus_gene_ensembl 78 Dec.2014 mm10 Mouse Mus musculus
Mustela putorius furo (Domestic ferret) Dec.2014v78 MusPutFur1.0 mfuro_gene_ensembl 78 Dec.2014 musFur1 Domestic ferret Mustela putorius furo
Myotis lucifugus (Microbat) May.2009v54 myoLuc1 mlucifugus_gene_ensembl 54 May.2009 myoLuc1 Microbat Myotis lucifugus
Myotis lucifugus (Microbat) Dec.2014v78 Myoluc2.0 mlucifugus_gene_ensembl 78 Dec.2014 myoLuc2 Microbat Myotis lucifugus
Nomascus leucogenys (Gibbon) Dec.2014v78 Nleu1.0 nleucogenys_gene_ensembl 78 Dec.2014 nomLeu1 Gibbon Nomascus leucogenys
Ochotona princeps (Pika) Dec.2014v78 OchPri2.0 oprinceps_gene_ensembl 78 Dec.2014 ochPri2 Pika Ochotona princeps
Ornithorhynchus anatinus (Platypus) Dec.2014v78 OANA5 oanatinus_gene_ensembl 78 Dec.2014 ornAna1 Platypus Ornithorhynchus anatinus
Oryctolagus cuniculus (Rabbit) May.2009v54 RABBIT ocuniculus_gene_ensembl 54 May.2009 oryCun1 Rabbit Oryctolagus cuniculus
Oryctolagus cuniculus (Rabbit) Dec.2014v78 OryCun2.0 ocuniculus_gene_ensembl 78 Dec.2014 oryCun2 Rabbit Oryctolagus cuniculus
Oryzias latipes (Medaka) Dec.2014v78 HdrR olatipes_gene_ensembl 78 Dec.2014 oryLat2 Medaka Oryzias latipes
Otolemur garnettii (Bushbaby) May.2009v54 otoGar1 ogarnettii_gene_ensembl 54 May.2009 otoGar1 Bushbaby Otolemur garnettii
Otolemur garnettii (Bushbaby) Dec.2014v78 OtoGar3 ogarnettii_gene_ensembl 78 Dec.2014 otoGar3 Bushbaby Otolemur garnettii
Ovis aries (Sheep) Dec.2014v78 Oar_v3.1 oaries_gene_ensembl 78 Dec.2014 oviAri3 Sheep Ovis aries
Pan troglodytes (Chimp) May.2009v54 CHIMP2.1 ptroglodytes_gene_ensembl 54 May.2009 panTro2 Chimp Pan troglodytes
Pan troglodytes (Chimp) Dec.2014v78 CHIMP2.1.4 ptroglodytes_gene_ensembl 78 Dec.2014 panTro4 Chimp Pan troglodytes
Papio anubis (Olive Baboon) Dec.2014v78 PapAnu2.0 panubis_gene_ensembl 78 Dec.2014 papAnu2 Olive Baboon Papio anubis
Pelodiscus sinensis (Chinese softshell turtle) Dec.2014v78 PelSin_1.0 psinensis_gene_ensembl 78 Dec.2014 pelSin1 Chinese softshell turtle Pelodiscus sinensis
Petromyzon marinus (Lamprey) Dec.2014v78 Pmarinus_7.0 pmarinus_gene_ensembl 78 Dec.2014 petMar2 Lamprey Petromyzon marinus
Poecilia formosa (Amazon molly) Dec.2014v78 Poecilia_formosa-5.1.2 pformosa_gene_ensembl 78 Dec.2014 poeFor1 Amazon molly Poecilia formosa
Pongo abelii (Orangutan) Dec.2014v78 PPYG2 pabelii_gene_ensembl 78 Dec.2014 ponAbe2 Orangutan Pongo abelii
Procavia capensis (Rock hyrax) Dec.2014v78 proCap1 pcapensis_gene_ensembl 78 Dec.2014 proCap1 Rock hyrax Procavia capensis
Pteropus vampyrus (Megabat) Dec.2014v78 pteVam1 pvampyrus_gene_ensembl 78 Dec.2014 pteVam1 Megabat Pteropus vampyrus
Rattus norvegicus (Rat) May.2012v67 RGSC3.4 rnorvegicus_gene_ensembl 66 May.2012 rn4 Rat Rattus norvegicus
Rattus norvegicus (Rat) Dec.2014v78 Rnor_5.0 rnorvegicus_gene_ensembl 78 Dec.2014 rn5 Rat Rattus norvegicus
Rattus norvegicus (Rat) May.2015v80 Rnor_6.0 rnorvegicus_gene_ensembl 84 May.2015 rn6 Rat Rattus norvegicus
Saccharomyces cerevisiae Dec.2014v78 R64-1-1 scerevisiae_gene_ensembl 78 Dec.2014 sacCer3 Saccharomyces cerevisiae Saccharomyces cerevisiae
Sarcophilus harrisii (Tasmanian Devil) Dec.2014v78 Devil_refv7.0 sharrisii_gene_ensembl 78 Dec.2014 sarHar1 Tasmanian Devil Sarcophilus harrisii
Sorex araneus (Shrew) Dec.2014v78 sorAra1 saraneus_gene_ensembl 78 Dec.2014 sorAra1 Shrew Sorex araneus
Sus scrofa (Pig) May.2012v67 Sscrofa9 sscrofa_gene_ensembl 66 May.2009 susScr2 Pig Sus scrofa
Sus scrofa (Pig) Dec.2014v78 Sscrofa10.2 sscrofa_gene_ensembl 78 Dec.2014 susScr3 Pig Sus scrofa
Taeniopygia guttata (Zebra finch) Dec.2014v78 taeGut3.2.4 tguttata_gene_ensembl 78 Dec.2014 taeGut2 Zebra finch Taeniopygia guttata
Takifugu rubripes (Fugu) Dec.2014v78 FUGU4.0 trubripes_gene_ensembl 78 Dec.2014 fr2 Fugu Takifugu rubripes
Tarsius syrichta (Tarsier) Dec.2014v78 tarSyr1 syrichta_gene_ensembl 78 Dec.2014 tarSyr1 Tarsier Tarsius syrichta
Tetraodon nigroviridis (Tetraodon) Dec.2014v78 TETRAODON8.0 tnigroviridis_gene_ensembl 78 Dec.2014 tetNig2 Tetraodon Tetraodon nigroviridis
Tupaia belangeri (Tree Shrew) Dec.2014v78 tupBel1 tbelangeri_gene_ensembl 78 Dec.2014 tupBel1 Tree Shrew Tupaia belangeri
Tursiops truncatus (Dolphin) Dec.2014v78 turTru1 ttruncatus_gene_ensembl 78 Dec.2014 turTru1 Dolphin Tursiops truncatus
Vicugna pacos (Alpaca) Dec.2014v78 vicPac1 vpacos_gene_ensembl 78 Dec.2014 vicPac1 Alpaca Vicugna pacos
Xenopus tropicalis (Xenopus) May.2009v54 JGI4.1 xtropicalis_gene_ensembl 54 May.2009 xenTro2 Xenopus Xenopus tropicalis
Xenopus tropicalis (Xenopus) Dec.2014v78 JGI4.2 xtropicalis_gene_ensembl 78 Dec.2014 xenTro3 Xenopus Xenopus tropicalis
Xiphophorus maculatus (Platyfish) Dec.2014v78 Xipmac4.4.2 xmaculatus_gene_ensembl 78 Dec.2014 xipMac1 Platyfish Xiphophorus maculatus
\ No newline at end of file
+species dateversion value dataset version date ucscId speciesShort speciesLong
Ailuropoda melanoleuca (Panda) Dec.2014v78 ailMel1 amelanoleuca_gene_ensembl 78 Dec.2014 ailMel1 Panda Ailuropoda melanoleuca
Anas platyrhynchos (Duck) Dec.2014v78 BGI_duck_1.0 aplatyrhynchos_gene_ensembl 78 Dec.2014 anaPlat1 Duck Anas platyrhynchos
Anolis carolinensis (Anole lizard) May.2009v54 AnoCar1.0 acarolinensis_gene_ensembl 54 May.2009 anoCar1 Anole lizard Anolis carolinensis
Anolis carolinensis (Anole lizard) Dec.2014v78 AnoCar2.0 acarolinensis_gene_ensembl 78 Dec.2014 anoCar2 Anole lizard Anolis carolinensis
Astyanax mexicanus (Cave fish) Dec.2014v78 AstMex102 amexicanus_gene_ensembl 78 Dec.2014 astMex1 Cave fish Astyanax mexicanus
Bos taurus (Cow) May.2009v54 Btau_4.0 btaurus_gene_ensembl 54 May.2009 bosTau4 Cow Bos taurus
Bos taurus (Cow) Dec.2014v78 UMD3.1 btaurus_gene_ensembl 78 Dec.2014 bosTau6 Cow Bos taurus
Caenorhabditis elegans May.2009v54 WS190 celegans_gene_ensembl 54 May.2009 ce6 Caenorhabditis elegans Caenorhabditis elegans
Caenorhabditis elegans Aug.2010v59 WS210 celegans_gene_ensembl 59 Aug.2010 ce9 Caenorhabditis elegans Caenorhabditis elegans
Caenorhabditis elegans Oct.2012v69 WBcel215 celegans_gene_ensembl 69 Oct.2012 ce8 Caenorhabditis elegans Caenorhabditis elegans
Caenorhabditis elegans Dec.2014v78 WBcel235 celegans_gene_ensembl 78 Dec.2014 ce10 Caenorhabditis elegans Caenorhabditis elegans
Callithrix jacchus (Marmoset) Dec.2014v78 C_jacchus3.2.1 cjacchus_gene_ensembl 78 Dec.2014 calJac3 Marmoset Callithrix jacchus
Canis familiaris (Dog) May.2012v67 CanFam_2.0 cfamiliaris_gene_ensembl 66 May.2012 canFam2 Dog Canis familiaris
Canis familiaris (Dog) Dec.2014v78 CanFam3.1 cfamiliaris_gene_ensembl 78 Dec.2014 canFam3 Dog Canis familiaris
Cavia porcellus (Guinea Pig) Dec.2014v78 cavPor3 cporcellus_gene_ensembl 78 Dec.2014 cavPor3 Guinea Pig Cavia porcellus
Chlorocebus sabaeus (Vervet-AGM) Dec.2014v78 ChlSab1.1 csabaeus_gene_ensembl 78 Dec.2014 chlSab1 Vervet-AGM Chlorocebus sabaeus
Choloepus hoffmanni (Sloth) Dec.2014v78 choHof1 choffmanni_gene_ensembl 78 Dec.2014 choHof1 Sloth Choloepus hoffmanni
Ciona intestinalis Dec.2014v78 KH cintestinalis_gene_ensembl 78 Dec.2014 ci2 Ciona intestinalis Ciona intestinalis
Ciona savignyi Dec.2014v78 CSAV2.0 csavignyi_gene_ensembl 78 Dec.2014 cioSav2 Ciona savignyi Ciona savignyi
Danio rerio (Zebrafish) May.2009v54 Zv8 drerio_gene_ensembl 54 May.2009 danRer7 Zebrafish Danio rerio
Danio rerio (Zebrafish) Dec.2014v78 Zv9 drerio_gene_ensembl 78 Dec.2014 danRer6 Zebrafish Danio rerio
Dasypus novemcinctus (Armadillo) Dec.2011v65 ARMA dnovemcinctus_gene_ensembl 65 Dec.2011 dasNov3 Armadillo Dasypus novemcinctus
Dasypus novemcinctus (Armadillo) May.2012v67 dasNov2 dnovemcinctus_gene_ensembl 66 May.2012 dasNov2 Armadillo Dasypus novemcinctus
Dasypus novemcinctus (Armadillo) Dec.2014v78 Dasnov3.0 dnovemcinctus_gene_ensembl 78 Dec.2014 dasNov3 Armadillo Dasypus novemcinctus
Dipodomys ordii (Kangaroo rat) Dec.2014v78 dipOrd1 dordii_gene_ensembl 78 Dec.2014 dipOrd1 Kangaroo rat Dipodomys ordii
Drosophila melanogaster (Fly) Dec.2014v78 BDGP5 dmelanogaster_gene_ensembl 78 Dec.2014 dm3 Fly Drosophila melanogaster
Echinops telfairi (Tenrec) Dec.2014v78 TENREC etelfairi_gene_ensembl 78 Dec.2014 echTel2 Tenrec Echinops telfairi
Equus caballus (Horse) Dec.2014v78 EquCab2 ecaballus_gene_ensembl 78 Dec.2014 equCab2 Horse Equus caballus
Erinaceus europaeus (Hedgehog) Dec.2014v78 eriEur1 eeuropaeus_gene_ensembl 78 Dec.2014 eriEur1 Hedgehog Erinaceus europaeus
Felis catus (Cat) Dec.2014v78 Felis_catus_6.2 fcatus_gene_ensembl 78 Dec.2014 felCat5 Cat Felis catus
Ficedula albicollis (Collared flycatcher) Dec.2014v78 FicAlb_1.4 falbicollis_gene_ensembl 78 Dec.2014 ficAlb1 Collared flycatcher Ficedula albicollis
Gadus morhua (Cod) Dec.2014v78 gadMor1 gmorhua_gene_ensembl 78 Dec.2014 gadMor1 Cod Gadus morhua
Gallus gallus (Chicken) May.2012v67 WASHUC2 ggallus_gene_ensembl 66 May.2012 galGal3 Chicken Gallus gallus
Gallus gallus (Chicken) Dec.2014v78 Galgal4 ggallus_gene_ensembl 78 Dec.2014 galGal4 Chicken Gallus gallus
Gasterosteus aculeatus (Stickleback) Dec.2014v78 BROAD S1 gaculeatus_gene_ensembl 78 Dec.2014 gasAcu1 Stickleback Gasterosteus aculeatus
Gorilla gorilla (Gorilla) May.2009v54 gorGor1 ggorilla_gene_ensembl 54 May.2009 gorGor1 Gorilla Gorilla gorilla
Gorilla gorilla (Gorilla) Dec.2014v78 gorGor3.1 ggorilla_gene_ensembl 78 Dec.2014 gorGor3 Gorilla Gorilla gorilla
Homo sapiens (Human) May.2009v54 NCBI36 hsapiens_gene_ensembl 54 May.2009 hg18 Human Homo sapiens
Homo sapiens (Human) Feb.2014v75 GRCh37.p13 hsapiens_gene_ensembl 75 Feb.2014 hg19 Human Homo sapiens
Homo sapiens (Human) Dec.2014v78 GRCh38 hsapiens_gene_ensembl 78 Dec.2014 hg38 Human Homo sapiens
Ictidomys tridecemlineatus (Squirrel) May.2009v54 speTri1 stridecemlineatus_gene_ensembl 54 May.2009 speTri1 Squirrel Ictidomys tridecemlineatus
Ictidomys tridecemlineatus (Squirrel) Dec.2014v78 spetri2 itridecemlineatus_gene_ensembl 78 Dec.2014 speTri2 Squirrel Ictidomys tridecemlineatus
Latimeria chalumnae (Coelacanth) Dec.2014v78 LatCha1 lchalumnae_gene_ensembl 78 Dec.2014 latCha1 Coelacanth Latimeria chalumnae
Lepisosteus oculatus (Spotted gar) Dec.2014v78 LepOcu1 loculatus_gene_ensembl 78 Dec.2014 lepOcu1 Spotted gar Lepisosteus oculatus
Loxodonta africana (Elephant) May.2009v54 loxAfr2 lafricana_gene_ensembl 54 May.2009 loxAfr2 Elephant Loxodonta africana
Loxodonta africana (Elephant) Dec.2014v78 Loxafr3.0 lafricana_gene_ensembl 78 Dec.2014 loxAfr3 Elephant Loxodonta africana
Macaca mulatta (Macaque) Dec.2014v78 MMUL1.0 mmulatta_gene_ensembl 78 Dec.2014 mMul1 Macaque Macaca mulatta
Macropus eugenii (Wallaby) Dec.2014v78 Meug_1.0 meugenii_gene_ensembl 78 Dec.2014 macEug2 Wallaby Macropus eugenii
Meleagris gallopavo (Turkey) Dec.2014v78 Turkey_2.01 mgallopavo_gene_ensembl 78 Dec.2014 melGa1 Turkey Meleagris gallopavo
Microcebus murinus (Mouse lemur) Dec.2014v78 micMur1 mmurinus_gene_ensembl 78 Dec.2014 micMur1 Mouse lemur Microcebus murinus
Monodelphis domestica (Opossum) Dec.2014v78 monDom5 mdomestica_gene_ensembl 78 Dec.2014 monDom5 Opossum Monodelphis domestica
Mus musculus (Mouse) May.2012v67 NCBIM37 mmusculus_gene_ensembl 66 May.2012 mm9 Mouse Mus musculus
Mus musculus (Mouse) Dec.2014v78 GRCm38.p3 mmusculus_gene_ensembl 78 Dec.2014 mm10 Mouse Mus musculus
Mustela putorius furo (Domestic ferret) Dec.2014v78 MusPutFur1.0 mfuro_gene_ensembl 78 Dec.2014 musFur1 Domestic ferret Mustela putorius furo
Myotis lucifugus (Microbat) May.2009v54 myoLuc1 mlucifugus_gene_ensembl 54 May.2009 myoLuc1 Microbat Myotis lucifugus
Myotis lucifugus (Microbat) Dec.2014v78 Myoluc2.0 mlucifugus_gene_ensembl 78 Dec.2014 myoLuc2 Microbat Myotis lucifugus
Nomascus leucogenys (Gibbon) Dec.2014v78 Nleu1.0 nleucogenys_gene_ensembl 78 Dec.2014 nomLeu1 Gibbon Nomascus leucogenys
Ochotona princeps (Pika) Dec.2014v78 OchPri2.0 oprinceps_gene_ensembl 78 Dec.2014 ochPri2 Pika Ochotona princeps
Ornithorhynchus anatinus (Platypus) Dec.2014v78 OANA5 oanatinus_gene_ensembl 78 Dec.2014 ornAna1 Platypus Ornithorhynchus anatinus
Oryctolagus cuniculus (Rabbit) May.2009v54 RABBIT ocuniculus_gene_ensembl 54 May.2009 oryCun1 Rabbit Oryctolagus cuniculus
Oryctolagus cuniculus (Rabbit) Dec.2014v78 OryCun2.0 ocuniculus_gene_ensembl 78 Dec.2014 oryCun2 Rabbit Oryctolagus cuniculus
Oryzias latipes (Medaka) Dec.2014v78 HdrR olatipes_gene_ensembl 78 Dec.2014 oryLat2 Medaka Oryzias latipes
Otolemur garnettii (Bushbaby) May.2009v54 otoGar1 ogarnettii_gene_ensembl 54 May.2009 otoGar1 Bushbaby Otolemur garnettii
Otolemur garnettii (Bushbaby) Dec.2014v78 OtoGar3 ogarnettii_gene_ensembl 78 Dec.2014 otoGar3 Bushbaby Otolemur garnettii
Ovis aries (Sheep) Dec.2014v78 Oar_v3.1 oaries_gene_ensembl 78 Dec.2014 oviAri3 Sheep Ovis aries
Pan troglodytes (Chimp) May.2009v54 CHIMP2.1 ptroglodytes_gene_ensembl 54 May.2009 panTro2 Chimp Pan troglodytes
Pan troglodytes (Chimp) Dec.2014v78 CHIMP2.1.4 ptroglodytes_gene_ensembl 78 Dec.2014 panTro4 Chimp Pan troglodytes
Papio anubis (Olive Baboon) Dec.2014v78 PapAnu2.0 panubis_gene_ensembl 78 Dec.2014 papAnu2 Olive Baboon Papio anubis
Pelodiscus sinensis (Chinese softshell turtle) Dec.2014v78 PelSin_1.0 psinensis_gene_ensembl 78 Dec.2014 pelSin1 Chinese softshell turtle Pelodiscus sinensis
Petromyzon marinus (Lamprey) Dec.2014v78 Pmarinus_7.0 pmarinus_gene_ensembl 78 Dec.2014 petMar2 Lamprey Petromyzon marinus
Poecilia formosa (Amazon molly) Dec.2014v78 Poecilia_formosa-5.1.2 pformosa_gene_ensembl 78 Dec.2014 poeFor1 Amazon molly Poecilia formosa
Pongo abelii (Orangutan) Dec.2014v78 PPYG2 pabelii_gene_ensembl 78 Dec.2014 ponAbe2 Orangutan Pongo abelii
Procavia capensis (Rock hyrax) Dec.2014v78 proCap1 pcapensis_gene_ensembl 78 Dec.2014 proCap1 Rock hyrax Procavia capensis
Pteropus vampyrus (Megabat) Dec.2014v78 pteVam1 pvampyrus_gene_ensembl 78 Dec.2014 pteVam1 Megabat Pteropus vampyrus
Rattus norvegicus (Rat) May.2012v67 RGSC3.4 rnorvegicus_gene_ensembl 66 May.2012 rn4 Rat Rattus norvegicus
Rattus norvegicus (Rat) Dec.2014v78 Rnor_5.0 rnorvegicus_gene_ensembl 78 Dec.2014 rn5 Rat Rattus norvegicus
Rattus norvegicus (Rat) May.2015v80 Rnor_6.0 rnorvegicus_gene_ensembl 84 May.2015 rn6 Rat Rattus norvegicus
Saccharomyces cerevisiae Dec.2014v78 R64-1-1 scerevisiae_gene_ensembl 78 Dec.2014 sacCer3 Saccharomyces cerevisiae Saccharomyces cerevisiae
Sarcophilus harrisii (Tasmanian Devil) Dec.2014v78 Devil_refv7.0 sharrisii_gene_ensembl 78 Dec.2014 sarHar1 Tasmanian Devil Sarcophilus harrisii
Sorex araneus (Shrew) Dec.2014v78 sorAra1 saraneus_gene_ensembl 78 Dec.2014 sorAra1 Shrew Sorex araneus
Sus scrofa (Pig) May.2012v67 Sscrofa9 sscrofa_gene_ensembl 66 May.2009 susScr2 Pig Sus scrofa
Sus scrofa (Pig) Dec.2014v78 Sscrofa10.2 sscrofa_gene_ensembl 78 Dec.2014 susScr3 Pig Sus scrofa
Taeniopygia guttata (Zebra finch) Dec.2014v78 taeGut3.2.4 tguttata_gene_ensembl 78 Dec.2014 taeGut2 Zebra finch Taeniopygia guttata
Takifugu rubripes (Fugu) Dec.2014v78 FUGU4.0 trubripes_gene_ensembl 78 Dec.2014 fr2 Fugu Takifugu rubripes
Tarsius syrichta (Tarsier) Dec.2014v78 tarSyr1 syrichta_gene_ensembl 78 Dec.2014 tarSyr1 Tarsier Tarsius syrichta
Tetraodon nigroviridis (Tetraodon) Dec.2014v78 TETRAODON8.0 tnigroviridis_gene_ensembl 78 Dec.2014 tetNig2 Tetraodon Tetraodon nigroviridis
Tupaia belangeri (Tree Shrew) Dec.2014v78 tupBel1 tbelangeri_gene_ensembl 78 Dec.2014 tupBel1 Tree Shrew Tupaia belangeri
Tursiops truncatus (Dolphin) Dec.2014v78 turTru1 ttruncatus_gene_ensembl 78 Dec.2014 turTru1 Dolphin Tursiops truncatus
Vicugna pacos (Alpaca) Dec.2014v78 vicPac1 vpacos_gene_ensembl 78 Dec.2014 vicPac1 Alpaca Vicugna pacos
Xenopus tropicalis (Xenopus) May.2009v54 JGI4.1 xtropicalis_gene_ensembl 54 May.2009 xenTro2 Xenopus Xenopus tropicalis
Xenopus tropicalis (Xenopus) Dec.2014v78 JGI4.2 xtropicalis_gene_ensembl 78 Dec.2014 xenTro3 Xenopus Xenopus tropicalis
Xiphophorus maculatus (Platyfish) Dec.2014v78 Xipmac4.4.2 xmaculatus_gene_ensembl 78 Dec.2014 xipMac1 Platyfish Xiphophorus maculatus
diff --git a/inst/extdata/biomartVersionsNow.txt b/inst/extdata/biomartVersionsNow.txt
index ee9badd..ba97e3a 100644
--- a/inst/extdata/biomartVersionsNow.txt
+++ b/inst/extdata/biomartVersionsNow.txt
@@ -1 +1 @@
-species value dataset ucscId speciesShort speciesLong date version
Ailuropoda melanoleuca (Panda) ailMel1 amelanoleuca_gene_ensembl ailMel1 Panda Ailuropoda melanoleuca head NA
Anas platyrhynchos (Duck) BGI_duck_1.0 aplatyrhynchos_gene_ensembl anaPlat1 Duck Anas platyrhynchos head NA
Anolis carolinensis (Anole lizard) AnoCar2.0 acarolinensis_gene_ensembl anoCar2 Anole lizard Anolis carolinensis head NA
Astyanax mexicanus (Cave fish) AstMex102 amexicanus_gene_ensembl astMex1 Cave fish Astyanax mexicanus head NA
Bos taurus (Cow) UMD3.1 btaurus_gene_ensembl bosTau8 Cow Bos taurus head NA
Caenorhabditis elegans WBcel235 celegans_gene_ensembl ce11 Caenorhabditis elegans Caenorhabditis elegans head NA
Callithrix jacchus (Marmoset) C_jacchus3.2.1 cjacchus_gene_ensembl calJac3 Marmoset Callithrix jacchus head NA
Canis familiaris (Dog) CanFam3.1 cfamiliaris_gene_ensembl canFam3 Dog Canis familiaris head NA
Cavia porcellus (Guinea Pig) cavPor3 cporcellus_gene_ensembl cavPor3 Guinea Pig Cavia porcellus head NA
Chlorocebus sabaeus (Vervet-AGM) ChlSab1.1 csabaeus_gene_ensembl chlSab1 Vervet-AGM Chlorocebus sabaeus head NA
Choloepus hoffmanni (Sloth) choHof1 choffmanni_gene_ensembl choHof1 Sloth Choloepus hoffmanni head NA
Ciona intestinalis KH cintestinalis_gene_ensembl ci2 Ciona intestinalis Ciona intestinalis head NA
Ciona savignyi CSAV2.0 csavignyi_gene_ensembl cioSav2 Ciona savignyi Ciona savignyi head NA
Danio rerio (Zebrafish) GRCz10 drerio_gene_ensembl danRer10 Zebrafish Danio rerio head NA
Dasypus novemcinctus (Armadillo) Dasnov3.0 dnovemcinctus_gene_ensembl dasNov3 Armadillo Dasypus novemcinctus head NA
Dipodomys ordii (Kangaroo rat) dipOrd1 dordii_gene_ensembl dipOrd1 Kangaroo rat Dipodomys ordii head NA
Drosophila melanogaster (Fly) BDGP6 dmelanogaster_gene_ensembl dm6 Fly Drosophila melanogaster head NA
Echinops telfairi (Tenrec) TENREC etelfairi_gene_ensembl echTel2 Tenrec Echinops telfairi head NA
Equus caballus (Horse) EquCab2 ecaballus_gene_ensembl equCab2 Horse Equus caballus head NA
Erinaceus europaeus (Hedgehog) eriEur1 eeuropaeus_gene_ensembl eriEur1 Hedgehog Erinaceus europaeus head NA
Felis catus (Cat) Felis_catus_6.2 fcatus_gene_ensembl felCat5 Cat Felis catus head NA
Ficedula albicollis (Collared flycatcher) FicAlb_1.4 falbicollis_gene_ensembl ficAlb1 Collared flycatcher Ficedula albicollis head NA
Gadus morhua (Cod) gadMor1 gmorhua_gene_ensembl gadMor1 Cod Gadus morhua head NA
Gallus gallus (Chicken) Galgal4 ggallus_gene_ensembl galGal4 Chicken Gallus gallus head NA
Gasterosteus aculeatus (Stickleback) BROADS1 gaculeatus_gene_ensembl gasAcu1 Stickleback Gasterosteus aculeatus head NA
Gorilla gorilla (Gorilla) gorGor3.1 ggorilla_gene_ensembl gorGor3 Gorilla Gorilla gorilla head NA
Homo sapiens (Human) GRCh38.p7 hsapiens_gene_ensembl hg38 Human Homo sapiens head NA
Ictidomys tridecemlineatus (Squirrel) spetri2 itridecemlineatus_gene_ensembl speTri2 Squirrel Ictidomys tridecemlineatus head NA
Latimeria chalumnae (Coelacanth) LatCha1 lchalumnae_gene_ensembl latCha1 Coelacanth Latimeria chalumnae head NA
Lepisosteus oculatus (Spotted gar) LepOcu1 loculatus_gene_ensembl lepOcu1 Spotted gar Lepisosteus oculatus head NA
Loxodonta africana (Elephant) loxAfr3 lafricana_gene_ensembl loxAfr3 Elephant Loxodonta africana head NA
Macaca mulatta (Macaque) MMUL_1 mmulatta_gene_ensembl mMul1 Macaque Macaca mulatta head NA
Macropus eugenii (Wallaby) Meug_1.0 meugenii_gene_ensembl macEug2 Wallaby Macropus eugenii head NA
Meleagris gallopavo (Turkey) UMD2 mgallopavo_gene_ensembl melGa1 Turkey Meleagris gallopavo head NA
Microcebus murinus (Mouse lemur) micMur1 mmurinus_gene_ensembl micMur1 Mouse lemur Microcebus murinus head NA
Monodelphis domestica (Opossum) monDom5 mdomestica_gene_ensembl monDom5 Opossum Monodelphis domestica head NA
Mus musculus (Mouse) GRCm38.p4 mmusculus_gene_ensembl mm10 Mouse Mus musculus head NA
Mustela putorius furo (Domestic ferret) MusPutFur1.0 mfuro_gene_ensembl musFur1 Domestic ferret Mustela putorius furo head NA
Myotis lucifugus (Microbat) myoLuc2 mlucifugus_gene_ensembl myoLuc2 Microbat Myotis lucifugus head NA
Nomascus leucogenys (Gibbon) Nleu1.0 nleucogenys_gene_ensembl nomLeu1 Gibbon Nomascus leucogenys head NA
Ochotona princeps (Pika) OchPri2.0 oprinceps_gene_ensembl ochPri2 Pika Ochotona princeps head NA
Ornithorhynchus anatinus (Platypus) OANA5 oanatinus_gene_ensembl ornAna1 Platypus Ornithorhynchus anatinus head NA
Oryctolagus cuniculus (Rabbit) OryCun2.0 ocuniculus_gene_ensembl oryCun2 Rabbit Oryctolagus cuniculus head NA
Oryzias latipes (Medaka) HdrR olatipes_gene_ensembl oryLat2 Medaka Oryzias latipes head NA
Otolemur garnettii (Bushbaby) OtoGar3 ogarnettii_gene_ensembl otoGar3 Bushbaby Otolemur garnettii head NA
Ovis aries (Sheep) Oar_v3.1 oaries_gene_ensembl oviAri3 Sheep Ovis aries head NA
Pan troglodytes (Chimp) CHIMP2.1.4 ptroglodytes_gene_ensembl panTro4 Chimp Pan troglodytes head NA
Papio anubis (Olive Baboon) PapAnu2.0 panubis_gene_ensembl papAnu2 Olive Baboon Papio anubis head NA
Pelodiscus sinensis (Chinese softshell turtle) PelSin_1.0 psinensis_gene_ensembl pelSin1 Chinese softshell turtle Pelodiscus sinensis head NA
Petromyzon marinus (Lamprey) Pmarinus_7.0 pmarinus_gene_ensembl petMar2 Lamprey Petromyzon marinus head NA
Poecilia formosa (Amazon molly) PoeFor_5.1.2 pformosa_gene_ensembl poeFor1 Amazon molly Poecilia formosa head NA
Pongo abelii (Orangutan) PPYG2 pabelii_gene_ensembl ponAbe2 Orangutan Pongo abelii head NA
Procavia capensis (Rock hyrax) proCap1 pcapensis_gene_ensembl proCap1 Rock hyrax Procavia capensis head NA
Pteropus vampyrus (Megabat) pteVam1 pvampyrus_gene_ensembl pteVam1 Megabat Pteropus vampyrus head NA
Rattus norvegicus (Rat) Rnor_6.0 rnorvegicus_gene_ensembl rn6 Rat Rattus norvegicus head NA
Saccharomyces cerevisiae R64-1-1 scerevisiae_gene_ensembl sacCer3 Saccharomyces cerevisiae Saccharomyces cerevisiae head NA
Sarcophilus harrisii (Tasmanian Devil) DEVIL7.0 sharrisii_gene_ensembl sarHar1 Tasmanian Devil Sarcophilus harrisii head NA
Sorex araneus (Shrew) sorAra1 saraneus_gene_ensembl sorAra1 Shrew Sorex araneus head NA
Sus scrofa (Pig) Sscrofa10.2 sscrofa_gene_ensembl susScr3 Pig Sus scrofa head NA
Taeniopygia guttata (Zebra finch) taeGut3.2.4 tguttata_gene_ensembl taeGut2 Zebra finch Taeniopygia guttata head NA
Takifugu rubripes (Fugu) FUGU4.0 trubripes_gene_ensembl fr2 Fugu Takifugu rubripes head NA
Tarsius syrichta (Tarsier) tarSyr1 tsyrichta_gene_ensembl tarSyr1 Tarsier Tarsius syrichta head NA
Tetraodon nigroviridis (Tetraodon) TETRAODON8.0 tnigroviridis_gene_ensembl tetNig2 Tetraodon Tetraodon nigroviridis head NA
Tupaia belangeri (Tree Shrew) tupBel1 tbelangeri_gene_ensembl tupBel1 Tree Shrew Tupaia belangeri head NA
Tursiops truncatus (Dolphin) turTru1 ttruncatus_gene_ensembl turTru1 Dolphin Tursiops truncatus head NA
Vicugna pacos (Alpaca) vicPac1 vpacos_gene_ensembl vicPac1 Alpaca Vicugna pacos head NA
Xenopus tropicalis (Xenopus) JGI4.2 xtropicalis_gene_ensembl xenTro3 Xenopus Xenopus tropicalis head NA
Xiphophorus maculatus (Platyfish) Xipmac4.4.2 xmaculatus_gene_ensembl xipMac1 Platyfish Xiphophorus maculatus head NA
+species value dataset ucscId speciesShort speciesLong date version
Ailuropoda melanoleuca (Panda) ailMel1 amelanoleuca_gene_ensembl ailMel1 Panda Ailuropoda melanoleuca head NA
Anas platyrhynchos (Duck) BGI_duck_1.0 aplatyrhynchos_gene_ensembl anaPlat1 Duck Anas platyrhynchos head NA
Anolis carolinensis (Anole lizard) AnoCar2.0 acarolinensis_gene_ensembl anoCar2 Anole lizard Anolis carolinensis head NA
Astyanax mexicanus (Cave fish) AstMex102 amexicanus_gene_ensembl astMex1 Cave fish Astyanax mexicanus head NA
Bos taurus (Cow) UMD3.1 btaurus_gene_ensembl bosTau8 Cow Bos taurus head NA
Caenorhabditis elegans WBcel235 celegans_gene_ensembl ce11 Caenorhabditis elegans Caenorhabditis elegans head NA
Callithrix jacchus (Marmoset) C_jacchus3.2.1 cjacchus_gene_ensembl calJac3 Marmoset Callithrix jacchus head NA
Canis familiaris (Dog) CanFam3.1 cfamiliaris_gene_ensembl canFam3 Dog Canis familiaris head NA
Cavia porcellus (Guinea Pig) cavPor3 cporcellus_gene_ensembl cavPor3 Guinea Pig Cavia porcellus head NA
Chlorocebus sabaeus (Vervet-AGM) ChlSab1.1 csabaeus_gene_ensembl chlSab1 Vervet-AGM Chlorocebus sabaeus head NA
Choloepus hoffmanni (Sloth) choHof1 choffmanni_gene_ensembl choHof1 Sloth Choloepus hoffmanni head NA
Ciona intestinalis KH cintestinalis_gene_ensembl ci2 Ciona intestinalis Ciona intestinalis head NA
Ciona savignyi CSAV2.0 csavignyi_gene_ensembl cioSav2 Ciona savignyi Ciona savignyi head NA
Danio rerio (Zebrafish) GRCz10 drerio_gene_ensembl danRer10 Zebrafish Danio rerio head NA
Dasypus novemcinctus (Armadillo) Dasnov3.0 dnovemcinctus_gene_ensembl dasNov3 Armadillo Dasypus novemcinctus head NA
Dipodomys ordii (Kangaroo rat) dipOrd1 dordii_gene_ensembl dipOrd1 Kangaroo rat Dipodomys ordii head NA
Drosophila melanogaster (Fly) BDGP6 dmelanogaster_gene_ensembl dm6 Fly Drosophila melanogaster head NA
Echinops telfairi (Tenrec) TENREC etelfairi_gene_ensembl echTel2 Tenrec Echinops telfairi head NA
Equus caballus (Horse) EquCab2 ecaballus_gene_ensembl equCab2 Horse Equus caballus head NA
Erinaceus europaeus (Hedgehog) eriEur1 eeuropaeus_gene_ensembl eriEur1 Hedgehog Erinaceus europaeus head NA
Felis catus (Cat) Felis_catus_6.2 fcatus_gene_ensembl felCat5 Cat Felis catus head NA
Ficedula albicollis (Collared flycatcher) FicAlb_1.4 falbicollis_gene_ensembl ficAlb1 Collared flycatcher Ficedula albicollis head NA
Gadus morhua (Cod) gadMor1 gmorhua_gene_ensembl gadMor1 Cod Gadus morhua head NA
Gallus gallus (Chicken) Galgal4 ggallus_gene_ensembl galGal4 Chicken Gallus gallus head NA
Gasterosteus aculeatus (Stickleback) BROAD S1 gaculeatus_gene_ensembl gasAcu1 Stickleback Gasterosteus aculeatus head NA
Gorilla gorilla (Gorilla) gorGor3.1 ggorilla_gene_ensembl gorGor3 Gorilla Gorilla gorilla head NA
Homo sapiens (Human) GRCh38.p7 hsapiens_gene_ensembl hg38 Human Homo sapiens head NA
Ictidomys tridecemlineatus (Squirrel) spetri2 itridecemlineatus_gene_ensembl speTri2 Squirrel Ictidomys tridecemlineatus head NA
Latimeria chalumnae (Coelacanth) LatCha1 lchalumnae_gene_ensembl latCha1 Coelacanth Latimeria chalumnae head NA
Lepisosteus oculatus (Spotted gar) LepOcu1 loculatus_gene_ensembl lepOcu1 Spotted gar Lepisosteus oculatus head NA
Loxodonta africana (Elephant) loxAfr3 lafricana_gene_ensembl loxAfr3 Elephant Loxodonta africana head NA
Macaca mulatta (Macaque) MMUL_1 mmulatta_gene_ensembl mMul1 Macaque Macaca mulatta head NA
Macropus eugenii (Wallaby) Meug_1.0 meugenii_gene_ensembl macEug2 Wallaby Macropus eugenii head NA
Meleagris gallopavo (Turkey) UMD2 mgallopavo_gene_ensembl melGa1 Turkey Meleagris gallopavo head NA
Microcebus murinus (Mouse lemur) micMur1 mmurinus_gene_ensembl micMur1 Mouse lemur Microcebus murinus head NA
Monodelphis domestica (Opossum) monDom5 mdomestica_gene_ensembl monDom5 Opossum Monodelphis domestica head NA
Mus musculus (Mouse) GRCm38.p4 mmusculus_gene_ensembl mm10 Mouse Mus musculus head NA
Mustela putorius furo (Domestic ferret) MusPutFur1.0 mfuro_gene_ensembl musFur1 Domestic ferret Mustela putorius furo head NA
Myotis lucifugus (Microbat) myoLuc2 mlucifugus_gene_ensembl myoLuc2 Microbat Myotis lucifugus head NA
Nomascus leucogenys (Gibbon) Nleu1.0 nleucogenys_gene_ensembl nomLeu1 Gibbon Nomascus leucogenys head NA
Ochotona princeps (Pika) OchPri2.0 oprinceps_gene_ensembl ochPri2 Pika Ochotona princeps head NA
Ornithorhynchus anatinus (Platypus) OANA5 oanatinus_gene_ensembl ornAna1 Platypus Ornithorhynchus anatinus head NA
Oryctolagus cuniculus (Rabbit) OryCun2.0 ocuniculus_gene_ensembl oryCun2 Rabbit Oryctolagus cuniculus head NA
Oryzias latipes (Medaka) HdrR olatipes_gene_ensembl oryLat2 Medaka Oryzias latipes head NA
Otolemur garnettii (Bushbaby) OtoGar3 ogarnettii_gene_ensembl otoGar3 Bushbaby Otolemur garnettii head NA
Ovis aries (Sheep) Oar_v3.1 oaries_gene_ensembl oviAri3 Sheep Ovis aries head NA
Pan troglodytes (Chimp) CHIMP2.1.4 ptroglodytes_gene_ensembl panTro4 Chimp Pan troglodytes head NA
Papio anubis (Olive Baboon) PapAnu2.0 panubis_gene_ensembl papAnu2 Olive Baboon Papio anubis head NA
Pelodiscus sinensis (Chinese softshell turtle) PelSin_1.0 psinensis_gene_ensembl pelSin1 Chinese softshell turtle Pelodiscus sinensis head NA
Petromyzon marinus (Lamprey) Pmarinus_7.0 pmarinus_gene_ensembl petMar2 Lamprey Petromyzon marinus head NA
Poecilia formosa (Amazon molly) PoeFor_5.1.2 pformosa_gene_ensembl poeFor1 Amazon molly Poecilia formosa head NA
Pongo abelii (Orangutan) PPYG2 pabelii_gene_ensembl ponAbe2 Orangutan Pongo abelii head NA
Procavia capensis (Rock hyrax) proCap1 pcapensis_gene_ensembl proCap1 Rock hyrax Procavia capensis head NA
Pteropus vampyrus (Megabat) pteVam1 pvampyrus_gene_ensembl pteVam1 Megabat Pteropus vampyrus head NA
Rattus norvegicus (Rat) Rnor_6.0 rnorvegicus_gene_ensembl rn6 Rat Rattus norvegicus head NA
Saccharomyces cerevisiae R64-1-1 scerevisiae_gene_ensembl sacCer3 Saccharomyces cerevisiae Saccharomyces cerevisiae head NA
Sarcophilus harrisii (Tasmanian Devil) DEVIL7.0 sharrisii_gene_ensembl sarHar1 Tasmanian Devil Sarcophilus harrisii head NA
Sorex araneus (Shrew) sorAra1 saraneus_gene_ensembl sorAra1 Shrew Sorex araneus head NA
Sus scrofa (Pig) Sscrofa10.2 sscrofa_gene_ensembl susScr3 Pig Sus scrofa head NA
Taeniopygia guttata (Zebra finch) taeGut3.2.4 tguttata_gene_ensembl taeGut2 Zebra finch Taeniopygia guttata head NA
Takifugu rubripes (Fugu) FUGU4.0 trubripes_gene_ensembl fr2 Fugu Takifugu rubripes head NA
Tarsius syrichta (Tarsier) tarSyr1 tsyrichta_gene_ensembl tarSyr1 Tarsier Tarsius syrichta head NA
Tetraodon nigroviridis (Tetraodon) TETRAODON8.0 tnigroviridis_gene_ensembl tetNig2 Tetraodon Tetraodon nigroviridis head NA
Tupaia belangeri (Tree Shrew) tupBel1 tbelangeri_gene_ensembl tupBel1 Tree Shrew Tupaia belangeri head NA
Tursiops truncatus (Dolphin) turTru1 ttruncatus_gene_ensembl turTru1 Dolphin Tursiops truncatus head NA
Vicugna pacos (Alpaca) vicPac1 vpacos_gene_ensembl vicPac1 Alpaca Vicugna pacos head NA
Xenopus tropicalis (Xenopus) JGI4.2 xtropicalis_gene_ensembl xenTro3 Xenopus Xenopus tropicalis head NA
Xiphophorus maculatus (Platyfish) Xipmac4.4.2 xmaculatus_gene_ensembl xipMac1 Platyfish Xiphophorus maculatus head NA
diff --git a/inst/scripts/documentation.R b/inst/scripts/documentation.R
index 298f91f..02d73ef 100644
--- a/inst/scripts/documentation.R
+++ b/inst/scripts/documentation.R
@@ -700,6 +700,8 @@ details <- list(
"snRNA"="Character or integer scalar. Fill color for annotation objects of type 'snRNA'.",
"snRNA_pseudogene"="Character or integer scalar. Fill color for annotation objects of type 'snRNA_pseudogene'.",
"tRNA_pseudogene"="Character or integer scalar. Fill color for annotation objects of type 'tRNA_pseudogene'.",
+ "utr3"="Character or integer scalar. Fill color for annotation objects of type 'utr3'.",
+ "utr5"="Character or integer scalar. Fill color for annotation objects of type 'utr5'.",
"V_segment"="Character or integer scalar. Fill color for annotation objects of type 'V_segment'.",
"verbose"="Logical scalar. Report data loading events from Bioamart or retrieval from cache."
),
diff --git a/man/AlignedReadTrack-class.Rd b/man/AlignedReadTrack-class.Rd
index 0304b4c..4b3c9af 100644
--- a/man/AlignedReadTrack-class.Rd
+++ b/man/AlignedReadTrack-class.Rd
@@ -5,6 +5,7 @@
\alias{AlignedReadTrack}
\alias{[,AlignedReadTrack-method}
\alias{[,AlignedReadTrack,ANY,ANY-method}
+\alias{[,AlignedReadTrack,ANY,ANY,ANY-method}
\alias{coverage,AlignedReadTrack-method}
\alias{drawAxis,AlignedReadTrack-method}
\alias{drawGD,AlignedReadTrack-method}
@@ -20,11 +21,11 @@
DEVELOPMENT AND SUBJECT TO CHANGE)}
\description{
-
+
A class to represent short sequences that have been aligned to a
reference genome as they are typically generated in a next generation
sequencing experiment.
-
+
}
\section{Objects from the Class}{
@@ -46,25 +47,25 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{range}{An object of class \code{\linkS4class{GRanges}}, or a
\code{data.frame} which will be coerced into one in which case it
needs to contain at least the three columns:
-
+
\describe{
\item{}{\code{start}, \code{end}: the start and end coordinates
for the track items.}
-
+
\item{}{\code{strand}: the strand information for the track
items. It may be provided in the form \code{+} for the Watson
strand, \code{-} for the Crick strand or \code{*} for either one
of the two.}
-
+
}
-
+
Alternatively, the \code{range} argument may be missing, in which
case the relevant information has to be provided as individual
function arguments (see below).
-
+
}
-
+
\item{start, end, width}{Integer vectors, giving the start and the end
end coordinates for the individual track items, or their width. Two
of the three need to be specified, and have to be of equal length or
@@ -102,20 +103,20 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{\dots}{Additional items which will all be interpreted as further
display parameters.}
-
+
}
-
+
\value{
The return value of the constructor function is a new object of class
\code{AlignedReadTrack}.
-
+
}
\section{Slots}{
-
+
\describe{
-
+
\item{\code{coverage}:}{Object of class \code{"list"}, a list of
coverage vectors for the plus strand, the minus strand and for
both strands combined.}
@@ -149,31 +150,31 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{\code{imageMap}:}{Object of class
\code{\linkS4class{ImageMap}}, inherited from class
\code{\linkS4class{GdObject}}}
-
- }
+
+ }
}
\section{Extends}{
-
+
Class \code{"\linkS4class{StackedTrack}"}, directly.
-
+
Class \code{"\linkS4class{RangeTrack}"}, by class "StackedTrack",
distance2.
-
+
Class \code{"\linkS4class{GdObject}"}, by class "StackedTrack",
distance3.
-
+
}
\section{Methods}{
-
+
In the following code chunks, \code{obj} is considered to be an object
of class \code{AlignedReadTrack}.
-
+
\bold{\emph{Exported in the name space:}}
-
+
\describe{
-
+
\item{[}{\code{signature(x="AlignedReadTrack")}: subset the items in
the \code{AlignedReadTrack}. This is essentially similar to
subsetting of the \code{\linkS4class{GRanges}} object in the
@@ -183,127 +184,127 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\code{coverageOnly=FALSE}.
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{i}: subsetting indices}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{obj[1:5]}}
-
+
}
}
\item{subset}{\code{signature(x="AlignedReadTrack")}: subset a
\code{AlignedReadTrack} by coordinates and sort if necessary.
-
+
\emph{Usage:}
-
+
\code{subset(x, from, to, sort=FALSE, stacks=FALSE)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: the coordinates range to subset
to.}
-
+
\item{}{\code{sort}: sort the object after subsetting. Usually
not necessary.}
-
+
\item{}{\code{stacks}: recompute the stacking after subsetting
which can be expensive and is not always necessary.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{subset(obj, from=10, to=20)}}
-
+
\item{}{\code{subset(obj, from=10, to=20, sort=TRUE, stacks=FALSE)}}
}
}
-
+
\item{split}{\code{signature(x="AlignedReadTrack")}: split an
\code{AlignedReadTrack} object by an appropriate factor vector (or
another vector that can be coerced into one). The output of this
operation is a list of \code{AlignedReadTrack} objects.
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{f}: the splitting factor.}
-
+
\item{}{\code{\dots}: all further arguments are ignored.}
-
+
}
-
+
\emph{Usage:}
-
+
\code{split(x, f, ...)}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{split(obj, c("a", "a", "b", "c", "a"))}}
-
+
}
}
-
+
\item{coverage}{\code{signature(x="AlignedReadTrack")}: return the
coverage vector for one of the strands, or the combined vector.
\emph{Usage:}
-
+
\code{coverage(x, strand="*")}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{strand}: the selector for the strand, \code{+} for
the Watson strand, \code{-} for the Crick strand or \code{*}
for both strands.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{coveraget(obj)}}
-
+
\item{}{\code{coverage(obj, strand="-")}}
-
+
}
}
}
\bold{\emph{Internal methods:}}
-
+
\describe{
-
-
+
+
\item{setCoverage}{\code{signature(GdObject="AlignedReadTrack")}:
recompute the coverage on the plus and minus strand as well as for
the combined strands and update the respective slot.
-
+
\emph{Usage:}
-
+
\code{setCoverage(GdObject)}
\emph{Examples:}
-
+
\describe{
\item{}{\code{setCoverage(obj)}}
@@ -315,32 +316,32 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
to the title panel of a track.
\emph{Usage:}
-
+
\code{drawAxis(GdObject, from, to, subset=FALSE, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: compute axis range from the data
within a certain coordinates range only.}
\item{}{\code{subset}: subset the object prior to calculating
the axis ranges. Can be expensive and is not always needed.}
-
+
\item{}{\code{\dots}: all further arguments are ignored.}
-
+
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawAxis(obj)}}
-
+
}
}
-
+
\item{drawGD}{\code{signature(gdObject="AlignedReadTrack")}: plot the
object to a graphics device. The return value of this method is
the input object, potentially updated during the plotting
@@ -351,16 +352,16 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
graphical output is created. Since subsetting of the object can be
potentially costly, this can be switched off in case subsetting
has already been performed before or is not necessary.
-
+
\emph{Usage:}
\code{drawGD(GdObject, minBase, maxBase, prepare=FALSE,
subset=TRUE, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{minBase}, \code{maxBase}: the coordinate range to
plot.}
@@ -373,191 +374,191 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{}{\code{\dots}: all further arguments are ignored.}
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawGD(obj)}}
-
+
\item{}{\code{Gviz:::drawGD(obj, minBase=1, maxBase=100)}}
-
+
\item{}{\code{Gviz:::drawGD(obj, prepare=TRUE,
subset=FALSE)}}
-
+
}
}
\item{drawGrid}{\code{signature(GdObject="AlignedReadTrack")}: superpose a grid on top of a track.
\emph{Usage:}
-
+
\code{drawGrid(GdObject, from, to)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: draw grid within a certain
coordinates range. This needs to be supplied for the plotting
function to know the current genomic coordinates.}
-
+
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawGrid(obj, from=10, to=100)}}
-
+
}
}
-
+
\item{initialize}{\code{signature(.Object="AligendReadTrack")}:
initialize the object.}
\item{show}{\code{signature(object="AlignedReadTrack")}: show a
human-readable summary of the object.}
-
+
}
\bold{\emph{Inherited methods:}}
\describe{
-
+
\item{stacking}{\code{signature(GdObject="AlignedReadTrack")}: return
the current stacking type.
-
+
\emph{Usage:}
-
+
\code{stacking(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{stacking(obj)}}
}
}
-
+
\item{stacking<-}{\code{signature(GdObject="AlignedReadTrack",
value="character")}: set the object's stacking type to one in
\code{c(hide, dense, squish, pack,full)}.
-
+
\emph{Usage:}
-
+
\code{stacking<-(GdObject, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
\emph{Examples:}
-
+
\describe{
\item{}{\code{stacking(obj) <- "squish" }}
}
}
-
+
\item{setStacks}{\code{signature(GdObject="AlignedReadTrack")}:
recompute the stacks based on the available space and on the
object's track items and stacking settings.
-
+
\emph{Usage:}
-
+
\code{setStacks(GdObject, from, to)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: compute stacking within a
certain coordinates range. This needs to be supplied for the
plotting function to know the current genomic coordinates.}
-
+
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::setStacks(obj)}}
}
}
-
+
\item{stacks}{\code{signature(GdObject="AlignedReadTrack")}: return
the stack indices for each track item.
\emph{Usage:}
-
+
\code{stacks(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::stacks(obj)}}
}
}
-
+
\item{chromosome}{\code{signature(GdObject="AlignedReadTrack")}:
return the chromosome for which the track is defined.
-
+
\emph{Usage:}
-
+
\code{chromosome(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{chromosome(obj)}}
-
+
}
}
-
+
\item{chromosome<-}{\code{signature(GdObject="AlignedReadTrack")}:
replace the value of the track's chromosome. This has to be a
valid UCSC chromosome identifier or an integer or character
scalar that can be reasonably coerced into one.
-
+
\emph{Usage:}
-
+
\code{chromosome<-(GdObject, value)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{chromosome(obj) <- "chr12"}}
-
+
}
}
-
+
\item{start, end, width}{\code{signature(x="AlignedReadTrack")}: the
start or end coordinates of the track items, or their width in
genomic coordinates.
-
+
\emph{Usage:}
-
+
\code{start(x)}
\code{end(x)}
@@ -565,13 +566,13 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\code{width(x)}
\emph{Examples:}
-
+
\describe{
\item{}{\code{start(obj)}}
-
+
\item{}{\code{end(obj)}}
-
+
\item{}{\code{width(obj)}}
}
@@ -580,9 +581,9 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{start<-, end<-, width<-}{\code{signature(x="AlignedReadTrack")}:
replace the start or end coordinates of the track items, or their
width.
-
+
\emph{Usage:}
-
+
\code{start<-(x, value)}
\code{end<-(x, value)}
@@ -590,63 +591,63 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\code{width<-(x, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
\emph{Examples:}
-
+
\describe{
\item{}{\code{start(obj) <- 1:10}}
-
+
\item{}{\code{end(obj) <- 20:30}}
-
+
\item{}{\code{width(obj) <- 1}}
}
}
-
+
\item{position}{\code{signature(GdObject="AlignedReadTrack")}: the
arithmetic mean of the track item's coordionates, i.e.,
\code{(end(obj)-start(obj))/2}.
\emph{Usage:}
-
+
\code{position(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{position(obj)}}
}
}
-
+
\item{feature}{\code{signature(GdObject="AlignedReadTrack")}: return the
grouping information for track items. For certain sub-classes,
groups may be indicated by different color schemes when
plotting. See \code{\link{grouping}} or
\code{\linkS4class{AnnotationTrack}} and
\code{\linkS4class{GeneRegionTrack}} for details.
-
+
\emph{Usage:}
-
+
\code{feature(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{feature(obj)}}
}
}
-
+
\item{feature<-}{\code{signature(gdObject="AlignedReadTrack",
value="character")}: set the grouping information for track
items. This has to be a factor vector (or another type of vector
@@ -654,36 +655,36 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
items in the \code{AlignedReadTrack}. See \code{\link{grouping}} or
\code{\linkS4class{AnnotationTrack}} and
\code{\linkS4class{GeneRegionTrack}} for details.
-
+
\emph{Usage:}
-
+
\code{feature<-(GdObject, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{feature(obj) <- c("a", "a", "b", "c", "a")}}
}
}
-
- \item{genome}{\code{signature(x="AlignedReadTrack")}: return the track's genome.
-
+
+ \item{genome}{\code{signature(x="AlignedReadTrack")}: return the track's genome.
+
\emph{Usage:}
-
+
\code{genome(x)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{genome(obj)}}
@@ -694,23 +695,23 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{genome<-}{\code{signature(x="AlignedReadTrack")}: set the track's
genome. Usually this has to be a valid UCSC identifier, however
this is not formally enforced here.
-
+
\emph{Usage:}
-
+
\code{genome<-(x, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{genome(obj) <- "mm9"}}
}
@@ -718,122 +719,122 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{length}{\code{signature(x="AlignedReadTrack")}: return the number
of items in the track.
-
+
\emph{Usage:}
-
+
\code{length(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{length(obj)}}
}
}
-
+
\item{range}{\code{signature(x="AlignedReadTrack")}: return the genomic
coordinates for the track as an object of class
\code{\linkS4class{IRanges}}.
-
+
\emph{Usage:}
-
+
\code{range(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{range(obj)}}
}
}
-
+
\item{ranges}{\code{signature(x="AlignedReadTrack")}: return the genomic
coordinates for the track along with all additional annotation
information as an object of class \code{\linkS4class{GRanges}}.
-
+
\emph{Usage:}
-
+
\code{ranges(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{ranges(obj)}}
}
}
-
+
\item{strand}{\code{signature(x="AlignedReadTrack")}: return a vector of
strand specifiers for all track items, in the form '+' for the
Watson strand, '-' for the Crick strand or '*' for either of the
two.
-
+
\emph{Usage:}
-
+
\code{strand(x)}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{strand(obj)}}
}
}
-
+
\item{strand<-}{\code{signature(x="AlignedReadTrack")}: replace the
strand information for the track items. The replacement value
needs to be an appropriate scalar or vector of strand values.
-
+
\emph{Usage:}
-
+
\code{strand<-(x, value)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{strand(obj) <- "+"}}
}
}
-
+
\item{values}{\code{signature(x="AlignedReadTrack")}: return all
additional annotation information except for the genomic coordinates
for the track items as a data.frame.
-
+
\emph{Usage:}
-
+
\code{values(x)}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{values(obj)}}
}
}
-
+
\item{coerce}{\code{signature(from="AlignedReadTrack",
to="data.frame")}: coerce the \code{\linkS4class{GRanges}}
object in the \code{range} slot into a regular data.frame.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{as(obj, "data.frame")}}
}
@@ -843,113 +844,113 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
name="character")}: list the value of the display parameter
\code{name}. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{displayPars(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj, "col")}}
-
+
}
}
-
-
+
+
\item{displayPars}{\code{signature(x="AlignedReadTrack",
name="missing")}: list the value of all available display
parameters. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj)}}
}
}
-
+
\item{getPar}{\code{signature(x="AlignedReadTrack", name="character")}:
alias for the \code{displayPars} method. See
\code{\link{settings}} for details on display parameters and
customization.
\emph{Usage:}
-
+
\code{getPar(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj, "col")}}
}
}
-
+
\item{getPar}{\code{signature(x="AlignedReadTrack", name="missing")}:
alias for the \code{displayPars} method. See
\code{\link{settings}} for details on display parameters and
customization.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj)}}
}
}
-
+
\item{displayPars<-}{\code{signature(x="AlignedReadTrack",
value="list")}: set display parameters using the values of the
named list in \code{value}. See \code{\link{settings}} for details
on display parameters and customization.
-
+
\emph{Usage:}
-
+
\code{displayPars<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj) <- list(col="red", lwd=2)}}
}
}
-
+
\item{setPar}{\code{signature(x="AlignedReadTrack", value="character")}:
set the single display parameter \code{name} to \code{value}. Note
that display parameters in the \code{AlignedReadTrack} class are
pass-by-reference, so no re-assignmnet to the symbol \code{obj} is
necessary. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{setPar(x, name, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{name}: the name of the display parameter to set.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, "col", "red")}}
}
}
-
+
\item{setPar}{\code{signature(x="AlignedReadTrack", value="list")}: set
display parameters by the values of the named list in
\code{value}. Note that display parameters in the
@@ -957,62 +958,62 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
re-assignmnet to the symbol \code{obj} is necessary. See
\code{\link{settings}} for details on display parameters and
customization.
-
-
+
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, list(col="red", lwd=2))}}
}
}
-
+
\item{group}{\code{signature(GdObject="AlignedReadTrack")}: return
grouping information for the individual items in the track. Unless
overwritten in one of the sub-classes, this usualy returns
\code{NULL}.
-
+
\emph{Usage:}
-
+
\code{group(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{group(obj)}}
}
}
-
+
\item{names}{\code{signature(x="AlignedReadTrack")}: return the value of
the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj)}}
}
}
-
+
\item{names<-}{\code{signature(x="AlignedReadTrack", value="character")}:
set the value of the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj) <- "foo"}}
}
@@ -1020,15 +1021,15 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{coords}{\code{signature(ImageMap="AlignedReadTrack")}: return the
coordinates from the internal image map.
-
+
\emph{Usage:}
-
+
\code{coords(ImageMap)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{coords(obj)}}
}
@@ -1036,15 +1037,15 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
\item{tags}{\code{signature(x="AlignedReadTrack")}: return the tags from the
internal image map.
-
+
\emph{Usage:}
-
+
\code{tags(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{tags(obj)}}
}
@@ -1053,54 +1054,54 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
}
-\section{Display Parameters}{
+\section{Display Parameters}{
The following display parameters are set for objects of class
\code{AlignedReadTrack} upon instantiation, unless one or more of
them have already been set by one of the optional sub-class initializers,
which always get precedence over these global defaults. See
\code{\link{settings}} for details on setting graphical parameters
- for tracks. \describe{
+ for tracks. \describe{
\item{}{\code{collapse=FALSE}: collapse overlapping ranges and
- aggregate the underlying data.}
+ aggregate the underlying data.}
\item{}{\code{detail="coverage"}: the amount of detail to plot the
data. Either \code{coverage} to show the coverage only, or
\code{reads} to show individual reads. For large data sets the
latter can be very inefficient. Please note that \code{reads} is
only available when the object has been created with option
- \code{coverageOnly=FALSE}.}
+ \code{coverageOnly=FALSE}.}
\item{}{\code{fill="#0080ff"}: the fill color for the coverage
- indicator.}
+ indicator.}
\item{}{\code{size=NULL}: the relative size of the track. Defaults
to size selection based on the underlying data. Can be overridden
- in the \code{\link{plotTracks}} function.}
+ in the \code{\link{plotTracks}} function.}
\item{}{\code{type="histogram"}: the plot type, one or several in
\code{c("p","l", "b", "a", "s", "g", "r", "S", "smooth", "histogram",
"mountain", "polygon", "h", "boxplot", "gradient", "heatmap",
"horizon")}. See the 'Details' section in \code{\linkS4class{DataTrack}}
- for more information on the individual plotting types.}
+ for more information on the individual plotting types.}
- }
+ }
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
- plotting of \code{AlignedReadTrack} objects.
+ plotting of \code{AlignedReadTrack} objects.
- \describe{
+ \describe{
- \item{}{\code{\linkS4class{StackedTrack}}:
+ \item{}{\code{\linkS4class{StackedTrack}}:
- \describe{
+ \describe{
\item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse
the y-ordering of stacked items. I.e., features that are
plotted on the bottom-most stacks will be moved to the top-most
- stack and vice versa.}
+ stack and vice versa.}
\item{}{\code{stackHeight=0.75}: Numeric between 0 and 1.
Controls the vertical size and spacing between stacked
@@ -1109,158 +1110,158 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
E.g., a value of 0.5 means that half of the available vertical
drawing space (for each stacking line) is used for the glyphs,
and thus one quarter of the available space each is used for
- spacing above and below the glyph. Defaults to 0.75.}
+ spacing above and below the glyph. Defaults to 0.75.}
- }
+ }
- }
+ }
- \item{}{\code{\linkS4class{GdObject}}:
+ \item{}{\code{\linkS4class{GdObject}}:
- \describe{
+ \describe{
\item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ all track items.}
\item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
- for the title panel.}
+ for the title panel.}
\item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panel.}
+ scalar. The background color for the title panel.}
\item{}{\code{cex=1}: Numeric scalar. The overall font expansion
factor for all text and glyphs, unless a more specific
- definition exists.}
+ definition exists.}
\item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
factor for the axis annotation. Defaults to \code{NULL}, in
which case it is automatically determined based on the
- available space.}
+ available space.}
\item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to \code{NULL},
which means that the text size is automatically adjusted to
- the available space.}
+ the available space.}
\item{}{\code{col="#0080FF"}: Integer or character scalar.
Default line color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ there is a more specific control defined elsewhere.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ The font and line color for the y axis, if any.}
\item{}{\code{col.border.title="white"}: Integer or character
- scalar. The border color for the title panels.}
+ scalar. The border color for the title panels.}
\item{}{\code{col.frame="lightgray"}: Integer or character
scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
+ \code{col} parameter.}
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
- global \code{col} parameter.}
+ global \code{col} parameter.}
\item{}{\code{col.title="white"} \code{(Aliases: fontcolor.title)}:
- Integer or character scalar. The border color for the title panels}
+ Integer or character scalar. The border color for the title panels}
\item{}{\code{fontcolor="black"}: Integer or character scalar.
The font color for all text, unless a more specific definition
- exists.}
+ exists.}
\item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text, unless a more specific definition exists.}
+ font face for all text, unless a more specific definition exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
- The font face for the title panels.}
+ The font face for the title panels.}
\item{}{\code{fontfamily="sans"}: Integer or character scalar.
The font family for all text, unless a more specific definition
- exists.}
+ exists.}
\item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ scalar. The font family for the title panels.}
\item{}{\code{fontsize=12}: Numeric scalar. The font size for
- all text, unless a more specific definition exists.}
+ all text, unless a more specific definition exists.}
\item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ track when plotting.}
\item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ of a grid.}
\item{}{\code{h=-1}: Integer scalar. Parameter controlling the
number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text, unless a more specific definition exists.}
+ height for all text, unless a more specific definition exists.}
\item{}{\code{lty="solid"}: Numeric scalar. Default line type
setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
+ specific control defined elsewhere.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{lwd=1}: Numeric scalar. Default line width setting
for all plotting elements, unless there is a more specific
- control defined elsewhere.}
+ control defined elsewhere.}
\item{}{\code{lwd.border.title=1}: Integer scalar. The border
- width for the title panels.}
+ width for the title panels.}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{lwd.title=1}: Integer scalar. The border width
- for the title panels}
+ for the title panels}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
\item{}{\code{min.height=3}: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{min.width=1}: Numeric scalar. The minimum range
width in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
plotting coordinates in 3' -> 5' direction if \code{TRUE}.
- This will effectively mirror the plot on the vertical axis.}
+ This will effectively mirror the plot on the vertical axis.}
\item{}{\code{rotation=0}: The rotation angle for all text
- unless a more specific definiton exists.}
+ unless a more specific definiton exists.}
\item{}{\code{rotation.title=90} \code{(Aliases: rotation.title)}:
The rotation angle for the text in the title panel. Even
though this can be adjusted, the automatic resizing of the
- title panel will currently not work, so use at own risk.}
+ title panel will currently not work, so use at own risk.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
- implemented).}
+ implemented).}
\item{}{\code{showTitle=TRUE}: Boolean controlling whether to
plot a title panel. Although this can be set individually
@@ -1269,17 +1270,17 @@ stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)
placeholder in case any of the other tracks include a title.
The same holds true for axes. Note that the the title panel
background color could be set to transparent in order to
- completely hide it.}
+ completely hide it.}
\item{}{\code{v=-1}: Integer scalar. Parameter controlling the
number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
- }
+ }
- }
+ }
- }
+ }
}
@@ -1414,3 +1415,4 @@ as(arTrack, "data.frame")
+
diff --git a/man/AlignmentsTrack-class.Rd b/man/AlignmentsTrack-class.Rd
index ed2dc32..d2b14a4 100644
--- a/man/AlignmentsTrack-class.Rd
+++ b/man/AlignmentsTrack-class.Rd
@@ -1483,6 +1483,8 @@ AlignmentsTrack(range=NULL, start=NULL, end=NULL, width=NULL, strand, chromosome
\code{\linkS4class{RangeTrack}}
+ \code{\linkS4class{SequenceTrack}}
+
\code{\linkS4class{StackedTrack}}
\code{\link{collapsing}}
@@ -1564,3 +1566,4 @@ to=44946660)
+
diff --git a/man/AnnotationTrack-class.Rd b/man/AnnotationTrack-class.Rd
index d779cfb..8609617 100644
--- a/man/AnnotationTrack-class.Rd
+++ b/man/AnnotationTrack-class.Rd
@@ -1678,12 +1678,13 @@ AnnotationTrack(range=NULL, start=NULL, end=NULL, width=NULL, feature,
\code{\linkS4class{GRanges}}
+ \code{\linkS4class{GRangesList}}
+
\code{\linkS4class{ImageMap}}
\code{\linkS4class{IRanges}}
\code{\linkS4class{RangeTrack}}
-
\code{\linkS4class{StackedTrack}}
@@ -1698,6 +1699,7 @@ AnnotationTrack(range=NULL, start=NULL, end=NULL, width=NULL, feature,
\code{\link{plotTracks}}
\code{\link{settings}}
+
}
\examples{
@@ -1885,3 +1887,4 @@ plotTracks(deTrack)
+
diff --git a/man/BiomartGeneRegionTrack-class.Rd b/man/BiomartGeneRegionTrack-class.Rd
index 897848a..d74fa11 100644
--- a/man/BiomartGeneRegionTrack-class.Rd
+++ b/man/BiomartGeneRegionTrack-class.Rd
@@ -69,9 +69,10 @@ BiomartGeneRegionTrack(start, end, biomart, chromosome, strand, genome,
\item{filters}{A list of additional filters to be applied in the
Biomart query. See \code{\link{getBM}} for details.}
- \item{featureMap}{Named character vector to map between the fields in
+ \item{featureMap}{Named character vector or list to map between the fields in
the Biomart data base and the features as they are used to construct
- the track.}
+ the track. If multiple values are provided in a single list item,
+ the package will use the first one that is defined in the selected Biomart.}
\item{name}{Character scalar of the track's name used in the title
panel when plotting.}
@@ -1229,328 +1230,409 @@ BiomartGeneRegionTrack(start, end, biomart, chromosome, strand, genome,
}
-\section{Display Parameters}{
+\section{Display Parameters}{
The following display parameters are set for objects of class
\code{BiomartGeneRegionTrack} upon instantiation, unless one or more
of them have already been set by one of the optional sub-class
initializers, which always get precedence over these global defaults.
See \code{\link{settings}} for details on setting graphical parameters
- for tracks. \describe{
+ for tracks. \describe{
\item{}{\code{C_segment="burlywood4"}: Character or integer scalar.
- Fill color for annotation objects of type 'C_segment'.}
+ Fill color for annotation objects of type 'C_segment'.}
\item{}{\code{D_segment="lightblue"}: Character or integer scalar.
- Fill color for annotation objects of type 'C_segment'.}
+ Fill color for annotation objects of type 'C_segment'.}
\item{}{\code{J_segment="dodgerblue2"}: Character or integer scalar.
- Fill color for annotation objects of type 'C_segment'.}
+ Fill color for annotation objects of type 'C_segment'.}
\item{}{\code{miRNA="cornflowerblue"}: Character or integer scalar.
- Fill color for annotation objects of type 'L_segment'.}
+ Fill color for annotation objects of type 'L_segment'.}
\item{}{\code{miRNA_pseudogene="cornsilk"}: Character or integer
- scalar. Fill color for annotation objects of type 'miRNA_pseudogene'.}
+ scalar. Fill color for annotation objects of type 'miRNA_pseudogene'.}
\item{}{\code{misc_RNA="cornsilk3"}: Character or integer scalar.
- Fill color for annotation objects of type 'misc_RNA'.}
+ Fill color for annotation objects of type 'misc_RNA'.}
\item{}{\code{misc_RNA_pseudogene="cornsilk4"}: Character or integer
- scalar. Fill color for annotation objects of type 'misc_RNA_pseudogene'.}
+ scalar. Fill color for annotation objects of type 'misc_RNA_pseudogene'.}
\item{}{\code{Mt_rRNA="yellow"}: Character or integer scalar. Fill
- color for annotation objects of type 'Mt_rRNA'.}
+ color for annotation objects of type 'Mt_rRNA'.}
\item{}{\code{Mt_tRNA="darkgoldenrod"}: Character or integer scalar.
- Fill color for annotation objects of type 'Mt_tRNA'.}
+ Fill color for annotation objects of type 'Mt_tRNA'.}
\item{}{\code{Mt_tRNA_pseudogene="darkgoldenrod1"}: Character or
integer scalar. Fill color for annotation objects of type
- 'Mt_tRNA_pseudogene'.}
+ 'Mt_tRNA_pseudogene'.}
- \item{}{\code{protein_coding="gold4"}: Character or integer scalar.
- Fill color for annotation objects of type 'protein_coding'.}
+ \item{}{\code{protein_coding="#FFD58A"}: Character or integer
+ scalar. Fill color for annotation objects of type 'protein_coding'.}
\item{}{\code{pseudogene="brown1"}: Character or integer scalar.
- Fill color for annotation objects of type 'pseudogene'.}
+ Fill color for annotation objects of type 'pseudogene'.}
\item{}{\code{retrotransposed="blueviolet"}: Character or integer
- scalar. Fill color for annotation objects of type 'retrotransposed'.}
+ scalar. Fill color for annotation objects of type 'retrotransposed'.}
\item{}{\code{rRNA="darkolivegreen1"}: Character or integer scalar.
- Fill color for annotation objects of type 'rRNA'.}
+ Fill color for annotation objects of type 'rRNA'.}
\item{}{\code{rRNA_pseudogene="darkolivegreen"}: Character or
integer scalar. Fill color for annotation objects of type
- 'rRNA_pseudogene'.}
+ 'rRNA_pseudogene'.}
- \item{}{\code{scRNA="darkorange"}: Character or integer scalar.
- Fill color for annotation objects of type 'scRNA'.}
+ \item{}{\code{scRNA="gold4"}: Character or integer scalar. Fill
+ color for annotation objects of type 'scRNA'.}
\item{}{\code{scRNA_pseudogene="darkorange2"}: Character or integer
- scalar. Fill color for annotation objects of type 'scRNA_pseudogene'.}
+ scalar. Fill color for annotation objects of type 'scRNA_pseudogene'.}
\item{}{\code{snoRNA="cyan"}: Character or integer scalar. Fill
- color for annotation objects of type 'snoRNA'.}
+ color for annotation objects of type 'snoRNA'.}
\item{}{\code{snoRNA_pseudogene="cyan2"}: Character or integer
- scalar. Fill color for annotation objects of type 'snoRNA_pseudogene'.}
+ scalar. Fill color for annotation objects of type 'snoRNA_pseudogene'.}
\item{}{\code{snRNA="coral"}: Character or integer scalar. Fill
- color for annotation objects of type 'snRNA'.}
+ color for annotation objects of type 'snRNA'.}
\item{}{\code{snRNA_pseudogene="coral3"}: Character or integer
- scalar. Fill color for annotation objects of type 'snRNA_pseudogene'.}
+ scalar. Fill color for annotation objects of type 'snRNA_pseudogene'.}
\item{}{\code{tRNA_pseudogene="antiquewhite3"}: Character or integer
- scalar. Fill color for annotation objects of type 'tRNA_pseudogene'.}
+ scalar. Fill color for annotation objects of type 'tRNA_pseudogene'.}
+
+ \item{}{\code{utr3="#FFD58A"}: FIXME: PLEASE ADD PARAMETER
+ DESCRIPTION.}
+
+ \item{}{\code{utr5="#FFD58A"}: FIXME: PLEASE ADD PARAMETER
+ DESCRIPTION.}
\item{}{\code{V_segment="aquamarine"}: Character or integer scalar.
- Fill color for annotation objects of type 'V_segment'.}
+ Fill color for annotation objects of type 'V_segment'.}
- }
+ \item{}{\code{verbose=FALSE}: Logical scalar. Report data loading
+ events from Bioamart or retrieval from cache.}
+
+ }
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
- plotting of \code{BiomartGeneRegionTrack} objects.
+ plotting of \code{BiomartGeneRegionTrack} objects.
- \describe{
+ \describe{
- \item{}{\code{\linkS4class{GeneRegionTrack}}:
+ \item{}{\code{\linkS4class{GeneRegionTrack}}:
- \describe{
+ \describe{
+
+ \item{}{\code{arrowHeadMaxWidth=20}: Numeric scalar. The maximum
+ width of the arrow head in pixels if \code{shape} is \code{arrow}.}
+
+ \item{}{\code{arrowHeadWidth=10}: Numeric scalar. The width of
+ the arrow head in pixels if \code{shape} is \code{fixedArrow}.}
+
+ \item{}{\code{col=NULL}: Character or integer scalar. The border
+ color for all track items. Defaults to using the same color
+ as in \code{fill}, also taking into account different track
+ \code{features}.}
+
+ \item{}{\code{collapseTranscripts=FALSE}: Logical or character
+ scalar. Can be one in \code{gene}, \code{longest}, \code{shortest}
+ or \code{meta}. Merge all transcripts of the same gene into
+ one single gene model. In the case of \code{gene} (or
+ \code{TRUE}), this will only keep the start location of the
+ first exon and the end location of the last exon from all
+ transcripts of the gene. For \code{shortest} and \code{longest},
+ only the longest or shortest transcript model is retained.
+ For \code{meta}, a meta-transcript containing the union of
+ all exons is formed (essentially identical to the operation
+ \code{reduce(geneModel)}).}
+
+ \item{}{\code{exonAnnotation=NULL}: Character scalar. Add
+ annotation information to the individual exon models. This
+ can be a value in \code{symbol}, \code{gene}, \code{transcript},
+ \code{exon} or \code{feature}. Defaults to \code{exon}. Only
+ works if \code{showExonId} is not \code{FALSE}.}
\item{}{\code{fill="orange"}: Character or integer scalar. The
fill color for untyped items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ grouped items. See \code{\link{grouping}} for details.}
- \item{}{\code{geneSymbols=TRUE}: Logical scalar. Use human-readable
- gene symbols or gene IDs for the transcript annotation.}
+ \item{}{\code{min.distance=0}: Numeric scalar. The minimum
+ pixel distance before collapsing range items, only if
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for
+ details. Note that a value larger than 0 may lead to UTR
+ regions being merged to CDS regions, which in most cases is
+ not particularly useful.}
\item{}{\code{shape=c("smallArrow", "box")}: Character scalar.
The shape in which to display the track items. Currently only
\code{box}, \code{arrow}, \code{ellipse}, and \code{smallArrow}
- are implemented.}
-
- \item{}{\code{showExonId=FALSE}: Logical scalar. Control whether
- to plot the individual exon identifiers.}
-
- \item{}{\code{collapseTranscripts=FALSE}: Logical or character
- scalar. Can be one in \code{gene}, \code{longest}, \code{shortest}
- or \code{meta}. Merge all
- transcripts of the same gene into one single gene
- model. In the case of \code{gene} (or \code{TRUE}), this will only keep the start location of the
- first exon and the end location of the last exon from all
- transcripts of the gene. For \code{shortest} and \code{longest},
- only the longest or shortest transcript model is retained. For
- \code{meta}, a meta-transcript containing the union of all exons
- is formed (essentially identical to the operation
- \code{reduce(geneModel)}).
- }
+ are implemented.}
- \item{}{\code{thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5",
- "miRNA", "lincRNA")}: Character vector. A listing of feature
- types that should be drawn with thin boxes. Typically those
- are non-coding elements.}
+ \item{}{\code{showExonId=NULL}: Logical scalar. Control whether
+ to plot the individual exon identifiers.}
- }
+ \item{}{\code{thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5",
+ "3UTR", "5UTR", "miRNA", "lincRNA", "three_prime_UTR",
+ "five_prime_UTR")}: Character vector. A listing of feature
+ types that should be drawn with thin boxes. Typically those
+ are non-coding elements.}
- }
+ \item{}{\code{transcriptAnnotation=NULL} \code{(Aliases:
+ transcriptAnnotation)}: Character scalar. Add annotation
+ information as transcript labels. This can be a value in
+ \code{symbol}, \code{gene}, \code{transcript}, \code{exon}
+ or \code{feature}. Defaults to \code{symbol}. Only works if
+ \code{showId} is not \code{FALSE}.}
- \item{}{\code{\linkS4class{AnnotationTrack}}:
+ }
- \describe{
+ }
+
+ \item{}{\code{\linkS4class{AnnotationTrack}}:
+
+ \describe{
\item{}{\code{cex=1}: Numeric scalar. The font expansion factor
- for item identifiers.}
+ for item identifiers.}
\item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion
- factor for the group-level annotation.}
+ factor for the group-level annotation.}
- \item{}{\code{col="transparent"}: Character or integer scalar.
- The border color for all track items.}
+ \item{}{\code{col.line="darkgray"}: Character scalar. The color
+ used for connecting lines between grouped items. Defaults to
+ a light gray, but if set to \code{NULL} the same color as
+ for the first item in the group is used.}
- \item{}{\code{fontcolor="white"}: Character or integer scalar.
- The font color for item identifiers.}
+ \item{}{\code{featureAnnotation=NULL}: Character scalar. Add
+ annotation information to the individual track elements. This
+ can be a value in \code{id}, \code{group} or \code{feature}.
+ Defaults to \code{id}. Only works if \code{showFeatureId} is
+ not \code{FALSE}.}
- \item{}{\code{fontcolor.group="#808080"}: Character or integer
- scalar. The font color for the group-level annotation.}
+ \item{}{\code{fontcolor.group="#808080"} \code{(Aliases:
+ fontcolor.group)}: Character or integer scalar. The font
+ color for the group-level annotation.}
- \item{}{\code{fontface=1}: Integer scalar. The font face for
- item identifiers.}
+ \item{}{\code{fontcolor.item="white"} \code{(Aliases:
+ fontcolor.item)}: Character or integer scalar. The font color
+ for item identifiers.}
\item{}{\code{fontface.group=2}: Numeric scalar. The font face
- for the group-level annotation.}
+ for the group-level annotation.}
- \item{}{\code{fontfamily="sans"}: Character scalar. The font
- family for item identifiers.}
+ \item{}{\code{fontfamily.group="sans"}: Character scalar. The
+ font family for the group-level annotation.}
- \item{}{\code{fontsize=12}: Numeric scalar. The font size for
- item identifiers.}
+ \item{}{\code{fontsize.group=12}: Numeric scalar. The font size
+ for the group-level annotation.}
+
+ \item{}{\code{groupAnnotation=NULL}: Character scalar. Add
+ annotation information as group labels. This can be a value
+ in \code{id}, \code{group} or \code{feature}. Defaults to
+ \code{group}. Only works if \code{showId} is not \code{FALSE}.}
+
+ \item{}{\code{just.group="left"} \code{(Aliases: just.group)}:
+ Character scalar. the justification of group labels. Either
+ \code{left}, \code{right}, \code{above} or \code{below}.}
\item{}{\code{lex=1}: Numeric scalar. The line expansion factor
for all track items. This is also used to connect grouped
- items. See \code{\link{grouping}} for details.}
+ items. See \code{\link{grouping}} for details.}
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for item identifiers.}
+ height for item identifiers.}
\item{}{\code{lty="solid"}: Character or integer scalar. The
line type for all track items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ grouped items. See \code{\link{grouping}} for details.}
\item{}{\code{lwd=1}: Integer scalar. The line width for all
track items. This is also used to connect grouped items. See
- \code{\link{grouping}} for details.}
+ \code{\link{grouping}} for details.}
+
+ \item{}{\code{mergeGroups=FALSE}: Logical scalar. Merge fully
+ overlapping groups if \code{collapse==TRUE}.}
+
+ \item{}{\code{min.height=3}: Numeric scalar. The minimum range
+ height in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details. For feathered bars indicating the strandedness
+ of grouped items this also controls the height of the arrow
+ feathers.}
+
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
\item{}{\code{rotation=0}: Numeric scalar. The degree of text
- rotation for item identifiers.}
+ rotation for item identifiers.}
+
+ \item{}{\code{rotation.group=0}: Numeric scalar. The degree of
+ text rotation for group labels.}
+
+ \item{}{\code{rotation.item=0}: Numeric scalar. The degree of
+ text rotation for item identifiers.}
\item{}{\code{showFeatureId=FALSE}: Logical scalar. Control
- whether to plot the individual track item identifiers.}
+ whether to plot the individual track item identifiers.}
\item{}{\code{showId=FALSE}: Logical scalar. Control whether
- to annotate individual groups.}
+ to annotate individual groups.}
\item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a
color gradient to show the amount of overplotting for collapsed
- items. This implies that \code{collapse==TRUE}}
+ items. This implies that \code{collapse==TRUE}}
\item{}{\code{size=1}: Numeric scalar. The relative size of
the track. Can be overridden in the \code{\link{plotTracks}}
- function.}
+ function.}
- \item{}{\code{mergeGroups=FALSE}: Logical scalar. Merge fully
- overlapping groups if \code{collapse==TRUE}.}
+ }
- }
+ }
- }
+ \item{}{\code{\linkS4class{StackedTrack}}:
- \item{}{\code{\linkS4class{StackedTrack}}:
+ \describe{
- \describe{
-
- \item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse the
- y-ordering of stacked items. I.e., features that are plotted on
- the bottom-most stacks will be moved to the top-most stack and
- vice versa.}
+ \item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse
+ the y-ordering of stacked items. I.e., features that are
+ plotted on the bottom-most stacks will be moved to the top-most
+ stack and vice versa.}
- \item{}{\code{stackHeight=0.75}: Numeric between 0 and 1. Controls
- the vertical size and spacing between stacked elements. The number
- defines the proportion of the total available space for the stack
- that is used to draw the glyphs. E.g., a value of 0.5 means that
- half of the available vertical drawing space (for each stacking
- line) is used for the glyphs, and thus one quarter of the available
- space each is used for spacing above and below the glyph. Defaults
- to 0.75.}
+ \item{}{\code{stackHeight=0.75}: Numeric between 0 and 1.
+ Controls the vertical size and spacing between stacked
+ elements. The number defines the proportion of the total
+ available space for the stack that is used to draw the glyphs.
+ E.g., a value of 0.5 means that half of the available vertical
+ drawing space (for each stacking line) is used for the glyphs,
+ and thus one quarter of the available space each is used for
+ spacing above and below the glyph. Defaults to 0.75.}
- }
+ }
- }
+ }
- \item{}{\code{\linkS4class{GdObject}}:
+ \item{}{\code{\linkS4class{GdObject}}:
- \describe{
+ \describe{
\item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ all track items.}
+
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
\item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panels.}
-
-
- \item{}{\code{col.border.title="transparent"}: Integer or character
- scalar. The border color for the title panels.}
-
- \item{}{\code{lwd.border.title=1}: Integer scalar. The border
- width for the title panels.}
-
+ scalar. The background color for the title panel.}
\item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ which case it is automatically determined based on the
+ available space.}
\item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to \code{NULL},
which means that the text size is automatically adjusted to
- the available space.}
+ the available space.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ The font and line color for the y axis, if any.}
+
+ \item{}{\code{col.border.title="white"}: Integer or character
+ scalar. The border color for the title panels.}
\item{}{\code{col.frame="lightgray"}: Integer or character
scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
-
- \item{}{\code{col.line=NULL}: Integer or character scalar.
- Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
+ \code{grid==TRUE}.}
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
- global \code{col} parameter.}
+ global \code{col} parameter.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{col.title="white"} \code{(Aliases: fontcolor.title)}:
+ Integer or character scalar. The border color for the title panels}
- \item{}{\code{collapse=TRUE}: Boolean controlling wether to
+ \item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
- details.}
+ details.}
+
+ \item{}{\code{fontcolor="black"}: Integer or character scalar.
+ The font color for all text, unless a more specific definition
+ exists.}
+
+ \item{}{\code{fontface=1}: Integer or character scalar. The
+ font face for all text, unless a more specific definition exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
- The font face for the title panels.}
+ The font face for the title panels.}
+
+ \item{}{\code{fontfamily="sans"}: Integer or character scalar.
+ The font family for all text, unless a more specific definition
+ exists.}
\item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ scalar. The font family for the title panels.}
+
+ \item{}{\code{fontsize=12}: Numeric scalar. The font size for
+ all text, unless a more specific definition exists.}
\item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ track when plotting.}
\item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ of a grid.}
\item{}{\code{h=-1}: Integer scalar. Parameter controlling the
number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
+
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ and when display parameter \code{grid==TRUE}.}
- \item{}{\code{min.distance=1}: Numeric scalar. The minimum
- pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
- \item{}{\code{min.height=3}: Numeric scalar. The minimum range
- height in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ \item{}{\code{rotation.title=90} \code{(Aliases: rotation.title)}:
+ The rotation angle for the text in the title panel. Even
+ though this can be adjusted, the automatic resizing of the
+ title panel will currently not work, so use at own risk.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
- implemented).}
+ implemented).}
\item{}{\code{showTitle=TRUE}: Boolean controlling whether to
plot a title panel. Although this can be set individually
@@ -1559,17 +1641,17 @@ BiomartGeneRegionTrack(start, end, biomart, chromosome, strand, genome,
placeholder in case any of the other tracks include a title.
The same holds true for axes. Note that the the title panel
background color could be set to transparent in order to
- completely hide it.}
+ completely hide it.}
\item{}{\code{v=-1}: Integer scalar. Parameter controlling the
number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
- }
+ }
- }
+ }
- }
+ }
}
@@ -1770,3 +1852,5 @@ tags(bmTrack)
+
+
diff --git a/man/CustomTrack-class.Rd b/man/CustomTrack-class.Rd
index 9eec5de..ace0a51 100644
--- a/man/CustomTrack-class.Rd
+++ b/man/CustomTrack-class.Rd
@@ -489,9 +489,14 @@ CustomTrack(plottingFunction=function(GdObject, prepare=FALSE, ...){}, variables
\code{\linkS4class{GdObject}}
-
\code{\linkS4class{ImageMap}}
+ \code{\link{collapsing}}
+
+ \code{\link{DataTrack}}
+
+ \code{\link{panel.grid}}
+
\code{\link{plotTracks}}
\code{\link{settings}}
@@ -530,3 +535,4 @@ CustomTrack(plottingFunction=function(GdObject, prepare=FALSE, ...){}, variables
+
diff --git a/man/DataTrack-class.Rd b/man/DataTrack-class.Rd
index 7f08a3e..489a9fa 100644
--- a/man/DataTrack-class.Rd
+++ b/man/DataTrack-class.Rd
@@ -5,6 +5,7 @@
\alias{DataTrack}
\alias{[,DataTrack-method}
\alias{[,DataTrack,ANY,ANY-method}
+\alias{[,DataTrack,ANY,ANY,ANY-method}
\alias{collapseTrack,DataTrack-method}
\alias{drawAxis,DataTrack-method}
\alias{drawGD,DataTrack-method}
@@ -1108,17 +1109,17 @@ name="DataTrack", importFunction, stream=FALSE, ...)
}
-\section{Display Parameters}{
+\section{Display Parameters}{
The following display parameters are set for objects of class
\code{DataTrack} upon instantiation, unless one or more of them have
already been set by one of the optional sub-class initializers, which
always get precedence over these global defaults. See \code{\link{settings}}
- for details on setting graphical parameters for tracks. \describe{
+ for details on setting graphical parameters for tracks. \describe{
\item{}{\code{aggregateGroups=FALSE}: Logical scalar. Aggregate
the values within a sample group using the aggregation funnction
- specified in the \code{aggregation} parameter.}
+ specified in the \code{aggregation} parameter.}
\item{}{\code{aggregation="mean"}: Function or character scalar.
Used to aggregate values in windows or for collapsing overlapping
@@ -1127,95 +1128,95 @@ name="DataTrack", importFunction, stream=FALSE, ...)
aggregated value. Alternatively, one of the predefined options
\code{mean}, \code{median} \code{sum}, \code{min}, \code{max} or
\code{extreme} can be supplied as a character scalar. Defaults
- to \code{mean}.}
+ to \code{mean}.}
\item{}{\code{alpha.confint=0.3}: Numeric scalar. The transparency
- for the confidence intervalls in confint-type plots.}
+ for the confidence intervalls in confint-type plots.}
\item{}{\code{amount=NULL}: Numeric scalar. Amount of jittering in
- xy-type plots. See \code{\link{panel.xyplot}} for details.}
+ xy-type plots. See \code{\link{panel.xyplot}} for details.}
\item{}{\code{baseline=NULL}: Numeric scalar. Y-axis position of
an optional baseline. This parameter has a special meaning for
mountain-type and polygon-type plots, see the 'Details' section
- in \code{\linkS4class{DataTrack}} for more information.}
+ in \code{\linkS4class{DataTrack}} for more information.}
\item{}{\code{box.legend=FALSE}: Logical scalar. Draw a box around
- a legend.}
+ a legend.}
\item{}{\code{box.ratio=1}: Numeric scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{box.width=NULL}: Numeric scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{cex=0.7}: Numeric scalar. The default pixel size for
- plotting symbols.}
+ plotting symbols.}
\item{}{\code{cex.legend=0.8}: Numeric scalar. The size factor for
- the legend text.}
+ the legend text.}
\item{}{\code{cex.sampleNames=NULL}: Numeric scalar. The size factor
for the sample names text in heatmap or horizon plots. Defaults
- to an automatic setting.}
+ to an automatic setting.}
\item{}{\code{coef=1.5}: Numeric scalar. Parameter controlling the
- boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{col=c("#0080ff", "#ff00ff", "darkgreen", "#ff0000",
"orange", "#00ff00", "brown")}: Character or integer vector. The
color used for all line and symbol elements, unless there is a
more specific control defined elsewhere. Unless \code{groups}
are specified, only the first color in the vector is usually
- regarded.}
+ regarded.}
\item{}{\code{col.baseline=NULL}: Character scalar. Color for the
- optional baseline, defaults to the setting of \code{col}.}
+ optional baseline, defaults to the setting of \code{col}.}
\item{}{\code{col.confint}: Character vector. Border colors for
- the confidence intervals for confint-type plots.}
+ the confidence intervals for confint-type plots.}
\item{}{\code{col.histogram="#808080"}: Character scalar. Line
- color in histogram-type plots.}
+ color in histogram-type plots.}
\item{}{\code{col.horizon}: The line color for the segments in the
\code{horizon}-type plot. See \code{\link{horizonplot}} for
- details.}
+ details.}
\item{}{\code{col.mountain=NULL}: Character scalar. Line color in
mountain-type and polygon-type plots, defaults to the setting of
- \code{col}.}
+ \code{col}.}
\item{}{\code{col.sampleNames="white"}: Character or integer scalar.
- The color used for the sample names in heatmap plots.}
+ The color used for the sample names in heatmap plots.}
\item{}{\code{collapse=FALSE}: Logical scalar. Collapse overlapping
- ranges and aggregate the underlying data.}
+ ranges and aggregate the underlying data.}
\item{}{\code{degree=1}: Numeric scalar. Parameter controlling the
loess calculation for smooth and mountain-type plots. See
- \code{\link{panel.loess}} for details.}
+ \code{\link{panel.loess}} for details.}
\item{}{\code{do.out=TRUE}: Logical scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{evaluation=50}: Numeric scalar. Parameter controlling
the loess calculation for smooth and mountain-type plots. See
- \code{\link{panel.loess}} for details.}
+ \code{\link{panel.loess}} for details.}
\item{}{\code{factor=0.5}: Numeric scalar. Factor to control amount
of jittering in xy-type plots. See \code{\link{panel.xyplot}}
- for details.}
+ for details.}
\item{}{\code{family="symmetric"}: Character scalar. Parameter
controlling the loess calculation for smooth and mountain-type
- plots. See \code{\link{panel.loess}} for details.}
+ plots. See \code{\link{panel.loess}} for details.}
\item{}{\code{fill.confint=NULL}: Character vector. Fill colors
- for the confidence intervals for confint-type plots.}
+ for the confidence intervals for confint-type plots.}
\item{}{\code{fill.histogram=NULL}: Character scalar. Fill color
- in histogram-type plots, defaults to the setting of \code{fill}.}
+ in histogram-type plots, defaults to the setting of \code{fill}.}
\item{}{\code{fill.horizon=c("#B41414", "#E03231", "#F7A99C",
"#9FC8DC", "#468CC8", "#0165B3")}: The fill colors for the segments
@@ -1223,23 +1224,23 @@ name="DataTrack", importFunction, stream=FALSE, ...)
six, where the first three entries are the colors for positive
changes, and the latter three entries are the colors for negative
changes. Defaults to a red-blue color scheme. See \code{\link{horizonplot}}
- for details.}
+ for details.}
\item{}{\code{fill.mountain=c("#CCFFFF", "#FFCCFF")}: Character
vector of length 2. Fill color in mountain-type and polygon-type
- plots.}
+ plots.}
\item{}{\code{fontcolor.legend="#808080"}: Integer or character
- scalar. The font color for the legend text.}
+ scalar. The font color for the legend text.}
\item{}{\code{fontface.legend=NULL}: Integer or character scalar.
- The font face for the legend text.}
+ The font face for the legend text.}
\item{}{\code{fontfamily.legend=NULL}: Integer or character scalar.
- The font family for the legend text.}
+ The font family for the legend text.}
\item{}{\code{fontsize.legend=NULL}: Numeric scalar. The pixel size
- for the legend text.}
+ for the legend text.}
\item{}{\code{gradient=c("#F7FBFF", "#DEEBF7", "#C6DBEF", "#9ECAE1",
"#6BAED6", "#4292C6", "#2171B5", "#08519C", "#08306B")}: Character
@@ -1248,115 +1249,115 @@ name="DataTrack", importFunction, stream=FALSE, ...)
with more than one group, the \code{col} parameter can be used
to control the group color scheme, however the gradient will
always be from white to 'col' and thus does not offer as much
- flexibility as this \code{gradient} parameter.}
+ flexibility as this \code{gradient} parameter.}
\item{}{\code{grid=FALSE}: Logical vector. Draw a line grid under
- the track content.}
+ the track content.}
\item{}{\code{groups=NULL}: Vector coercable to a factor. Optional
sample grouping. See 'Details' section in \code{\linkS4class{DataTrack}}
- for further information.}
+ for further information.}
\item{}{\code{horizon.origin=0}: The baseline relative to which
changes are indicated on the \code{horizon}-type plot. See
- \code{\link{horizonplot}} for details.}
+ \code{\link{horizonplot}} for details.}
\item{}{\code{horizon.scale=NULL}: The scale for each of the segments
in the \code{horizon}-type plot. Defaults to 1/3 of the absolute
- data range. See \code{\link{horizonplot}} for details.}
+ data range. See \code{\link{horizonplot}} for details.}
\item{}{\code{jitter.x=FALSE}: Logical scalar. Toggle on jittering
on the x axis in xy-type plots. See \code{\link{panel.xyplot}}
- for details.}
+ for details.}
\item{}{\code{jitter.y=FALSE}: Logical scalar. Toggle off jittering
on the y axis in xy-type plots. See \code{\link{panel.xyplot}}
- for details.}
+ for details.}
\item{}{\code{legend=TRUE}: Boolean triggering the addition of a
legend to the track to indicate groups. This only has an effect
- if at least two groups are present.}
+ if at least two groups are present.}
\item{}{\code{levels.fos=NULL}: Numeric scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{lineheight.legend=NULL}: Numeric scalar. The line
- height for the legend text.}
+ height for the legend text.}
\item{}{\code{lty.baseline=NULL}: Character or numeric scalar. Line
type of the optional baseline, defaults to the setting of
- \code{lty}.}
+ \code{lty}.}
\item{}{\code{lty.mountain=NULL}: Character or numeric scalar. Line
type in mountain-type and polygon-type plots, defaults to the
- setting of \code{lty}.}
+ setting of \code{lty}.}
\item{}{\code{lwd.baseline=NULL}: Numeric scalar. Line width of
- the optional baseline, defaults to the setting of \code{lwd}.}
+ the optional baseline, defaults to the setting of \code{lwd}.}
\item{}{\code{lwd.mountain=NULL}: Numeric scalar. Line width in
mountain-type and polygon-type plots, defaults to the setting of
- \code{lwd}.}
+ \code{lwd}.}
\item{}{\code{min.distance=0}: Numeric scalar. The mimimum distance
- in pixel below which to collapse ranges.}
+ in pixel below which to collapse ranges.}
\item{}{\code{na.rm=FALSE}: Boolean controlling whether to discard
- all NA values when plotting or to keep empty spaces for NAs}
+ all NA values when plotting or to keep empty spaces for NAs}
\item{}{\code{ncolor=100}: Integer scalar. The number of colors
- for the 'gradient' plotting type}
+ for the 'gradient' plotting type}
\item{}{\code{notch=FALSE}: Logical scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{notch.frac=0.5}: Numeric scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{pch=20}: Integer scalar. The type of glyph used for
- plotting symbols.}
+ plotting symbols.}
\item{}{\code{separator=0}: Numeric scalar. Number of pixels used
- to separate individual samples in heatmap- and horizon-type plots.}
+ to separate individual samples in heatmap- and horizon-type plots.}
\item{}{\code{showColorBar=TRUE}: Boolean. Indicate the data range
- color mapping in the axis for 'heatmap' or 'gradient' types.}
+ color mapping in the axis for 'heatmap' or 'gradient' types.}
\item{}{\code{showSampleNames=FALSE}: Boolean. Display the names
- of the individual samples in a heatmap or a horizon plot.}
+ of the individual samples in a heatmap or a horizon plot.}
\item{}{\code{size=NULL}: Numeric scalar. The relative size of the
track. Can be overridden in the \code{\link{plotTracks}} function.
By default the size will be set automatically based on the selected
- plotting type.}
+ plotting type.}
\item{}{\code{span=0.2}: Numeric scalar. Parameter controlling the
loess calculation for smooth and mountain-type plots. See
- \code{\link{panel.loess}} for details.}
+ \code{\link{panel.loess}} for details.}
\item{}{\code{stackedBars=TRUE}: Logical scalar. When there are
several data groups, draw the histogram-type plots as stacked
- barplots or grouped side by side.}
+ barplots or grouped side by side.}
\item{}{\code{stats=function}: Function. Parameter controlling the
- boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{transformation=NULL}: Function. Applied to the data
matrix prior to plotting or when calling the \code{score} method.
The function should accept exactly one input argument and its
return value needs to be a numeric vector which can be coerced
back into a data matrix of identical dimensionality as the input
- data.}
+ data.}
\item{}{\code{type="p"}: Character vector. The plot type, one or
several in \code{c("p","l", "b", "a", "a_confint", "s", "g", "r",
"S", "confint", "smooth", "histogram", "mountain", "polygon",
"h", "boxplot", "gradient", "heatmap", "horizon")}. See 'Details'
section in \code{\linkS4class{DataTrack}} for more information
- on the individual plotting types.}
+ on the individual plotting types.}
\item{}{\code{varwidth=FALSE}: Logical scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{window=NULL}: Numeric or character scalar. Aggregate
the rows values of the data matrix to \code{window} equally sized
@@ -1365,157 +1366,157 @@ name="DataTrack", importFunction, stream=FALSE, ...)
using the same aggregation method. Alternatively, the special
value \code{auto} causes the function to determine the optimal
window size to avoid overplotting, and \code{fixed} uses fixed-size
- windows of size \code{windowSize}.}
+ windows of size \code{windowSize}.}
\item{}{\code{windowSize=NULL}: Numeric scalar. The size of the
- running window when the value of \code{window} is negative.}
+ running window when the value of \code{window} is negative.}
\item{}{\code{ylim=NULL}: Numeric vector of length 2. The range of
- the y-axis scale.}
+ the y-axis scale.}
- }
+ }
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
- plotting of \code{DataTrack} objects.
+ plotting of \code{DataTrack} objects.
- \describe{
+ \describe{
- \item{}{\code{\linkS4class{GdObject}}:
+ \item{}{\code{\linkS4class{GdObject}}:
- \describe{
+ \describe{
\item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ all track items.}
\item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
- for the title panel.}
+ for the title panel.}
\item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panel.}
+ scalar. The background color for the title panel.}
\item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
factor for the axis annotation. Defaults to \code{NULL}, in
which case it is automatically determined based on the
- available space.}
+ available space.}
\item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to \code{NULL},
which means that the text size is automatically adjusted to
- the available space.}
+ the available space.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ The font and line color for the y axis, if any.}
\item{}{\code{col.border.title="white"}: Integer or character
- scalar. The border color for the title panels.}
+ scalar. The border color for the title panels.}
\item{}{\code{col.frame="lightgray"}: Integer or character
scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
+ \code{col} parameter.}
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
- global \code{col} parameter.}
+ global \code{col} parameter.}
\item{}{\code{col.title="white"} \code{(Aliases: fontcolor.title)}:
- Integer or character scalar. The border color for the title panels}
+ Integer or character scalar. The border color for the title panels}
\item{}{\code{fill="lightgray"}: Integer or character scalar.
Default fill color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ there is a more specific control defined elsewhere.}
\item{}{\code{fontcolor="black"}: Integer or character scalar.
The font color for all text, unless a more specific definition
- exists.}
+ exists.}
\item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text, unless a more specific definition exists.}
+ font face for all text, unless a more specific definition exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
- The font face for the title panels.}
+ The font face for the title panels.}
\item{}{\code{fontfamily="sans"}: Integer or character scalar.
The font family for all text, unless a more specific definition
- exists.}
+ exists.}
\item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ scalar. The font family for the title panels.}
\item{}{\code{fontsize=12}: Numeric scalar. The font size for
- all text, unless a more specific definition exists.}
+ all text, unless a more specific definition exists.}
\item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ track when plotting.}
\item{}{\code{h=-1}: Integer scalar. Parameter controlling the
number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text, unless a more specific definition exists.}
+ height for all text, unless a more specific definition exists.}
\item{}{\code{lty="solid"}: Numeric scalar. Default line type
setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
+ specific control defined elsewhere.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{lwd=1}: Numeric scalar. Default line width setting
for all plotting elements, unless there is a more specific
- control defined elsewhere.}
+ control defined elsewhere.}
\item{}{\code{lwd.border.title=1}: Integer scalar. The border
- width for the title panels.}
+ width for the title panels.}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{lwd.title=1}: Integer scalar. The border width
- for the title panels}
+ for the title panels}
\item{}{\code{min.height=3}: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{min.width=1}: Numeric scalar. The minimum range
width in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
plotting coordinates in 3' -> 5' direction if \code{TRUE}.
- This will effectively mirror the plot on the vertical axis.}
+ This will effectively mirror the plot on the vertical axis.}
\item{}{\code{rotation=0}: The rotation angle for all text
- unless a more specific definiton exists.}
+ unless a more specific definiton exists.}
\item{}{\code{rotation.title=90} \code{(Aliases: rotation.title)}:
The rotation angle for the text in the title panel. Even
though this can be adjusted, the automatic resizing of the
- title panel will currently not work, so use at own risk.}
+ title panel will currently not work, so use at own risk.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
- implemented).}
+ implemented).}
\item{}{\code{showTitle=TRUE}: Boolean controlling whether to
plot a title panel. Although this can be set individually
@@ -1524,17 +1525,17 @@ name="DataTrack", importFunction, stream=FALSE, ...)
placeholder in case any of the other tracks include a title.
The same holds true for axes. Note that the the title panel
background color could be set to transparent in order to
- completely hide it.}
+ completely hide it.}
\item{}{\code{v=-1}: Integer scalar. Parameter controlling the
number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
- }
+ }
- }
+ }
- }
+ }
}
@@ -1684,6 +1685,8 @@ name="DataTrack", importFunction, stream=FALSE, ...)
\code{\link{grouping}}
+ \code{\link{horizonplot}}
+
\code{\link{panel.bwplot}}
\code{\link{panel.grid}}
@@ -1815,3 +1818,4 @@ as(dtTrack, "data.frame")
+
diff --git a/man/DisplayPars-class.Rd b/man/DisplayPars-class.Rd
index 220b5cb..5e719c8 100644
--- a/man/DisplayPars-class.Rd
+++ b/man/DisplayPars-class.Rd
@@ -276,3 +276,4 @@ availableDisplayPars("GenomeAxisTrack")
+
diff --git a/man/GdObject-class.Rd b/man/GdObject-class.Rd
index 202c8a7..d70df66 100644
--- a/man/GdObject-class.Rd
+++ b/man/GdObject-class.Rd
@@ -591,6 +591,8 @@
\code{\link{DataTrack}}
+ \code{\link{grouping}}
+
\code{\link{panel.grid}}
\code{\link{plotTracks}}
@@ -639,3 +641,4 @@
+
diff --git a/man/GeneRegionTrack-class.Rd b/man/GeneRegionTrack-class.Rd
index df68fee..995e532 100644
--- a/man/GeneRegionTrack-class.Rd
+++ b/man/GeneRegionTrack-class.Rd
@@ -1462,7 +1462,7 @@ GeneRegionTrack(range=NULL, rstarts=NULL, rends=NULL, rwidths=NULL,
\item{}{\code{min.distance=0}: Numeric scalar. The minimum pixel
distance before collapsing range items, only if
- \\code{collapse==TRUE}. See \\code{\\link{collapsing}} for
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for
details. Note that a value larger than 0 may lead to UTR regions
being merged to CDS regions, which in most cases is not particularly
useful.}
@@ -1748,6 +1748,8 @@ GeneRegionTrack(range=NULL, rstarts=NULL, rends=NULL, rwidths=NULL,
\code{\linkS4class{StackedTrack}}
+ \code{\linkS4class{TxDb}}
+
\code{\link{collapsing}}
\code{\link{DataTrack}}
@@ -1916,3 +1918,4 @@ tags(grTrack)
+
diff --git a/man/GenomeAxisTrack-class.Rd b/man/GenomeAxisTrack-class.Rd
index aae2d07..5fd1f50 100644
--- a/man/GenomeAxisTrack-class.Rd
+++ b/man/GenomeAxisTrack-class.Rd
@@ -5,6 +5,7 @@
\alias{GenomeAxisTrack}
\alias{[,GenomeAxisTrack-method}
\alias{[,GenomeAxisTrack,ANY,ANY-method}
+\alias{[,GenomeAxisTrack,ANY,AN,ANY-method}
\alias{collapseTrack,GenomeAxisTrack-method}
\alias{drawGD,GenomeAxisTrack-method}
\alias{end,GenomeAxisTrack-method}
@@ -38,7 +39,7 @@ GenomeAxisTrack(range=NULL, name="Axis", id, ...)
}
\arguments{
-
+
\item{range}{Optional \code{\linkS4class{GRanges}} or
\code{\linkS4class{IRanges}} object to highlight certain regions on
the axis.}
@@ -53,15 +54,15 @@ GenomeAxisTrack(range=NULL, name="Axis", id, ...)
\item{\dots}{Additional items which will all be interpreted as further
display parameters. See \code{\link{settings}} and the "Display
Parameters" section below for details.}
-
+
}
\details{
-
+
A \code{GenomeAxisTrack} can be customized using the familiar display
parameters. By providing a \code{GRanges} or \code{IRanges} object to
the constructor, ranges on the axis can be further highlighted.\
-
+
With the \code{scale} display parameter, a small scale indicator can
be shown instead of the entire genomic axis. The scale can either be
provided as a fraction of the plotting region (it will be rounded to
@@ -71,30 +72,30 @@ GenomeAxisTrack(range=NULL, name="Axis", id, ...)
used insterad of the full axis. In particular, only the parameters
\code{exponent}, \code{alpha}, \code{lwd}, \code{col}, \code{cex},
\code{distFromAxis} and \code{labelPos} are used.
-
+
}
\value{
-
+
The return value of the constructor function is a new object of class
\code{GenomeAxisTrack}.
-
+
}
\section{Slots}{
\describe{
-
+
\item{\code{range}:}{Object of class \code{\linkS4class{GRanges}},
highlighted on the axis. }
\item{\code{dp}:}{Object of class
\code{\linkS4class{DisplayPars}}, inherited from class
\code{\linkS4class{GdObject}}}
-
+
\item{\code{name}:}{Object of class \code{"character"}, inherited
from class \code{\linkS4class{GdObject}}}
-
+
\item{\code{imageMap}:}{Object of class
\code{\linkS4class{ImageMap}}, inherited from class
\code{\linkS4class{GdObject}}}
@@ -107,29 +108,29 @@ Class \code{"\linkS4class{GdObject}"}, directly.
}
\section{Methods}{
-
+
In the following code chunks, \code{obj} is considered to be an object of class \code{GenomeAxisTrack}.
-
+
\bold{\emph{Exported in the name space:}}
-
+
\describe{
-
+
\item{[}{\code{signature(x="GenomeAxisTrack")}: subset the
\code{GRanges} object in the \code{range} slot. For most
applications, the \code{subset} method may be more appropriate.
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{i}: subsetting incides.}
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{obj[1:5]}}
}
@@ -138,57 +139,57 @@ Class \code{"\linkS4class{GdObject}"}, directly.
\item{start, end, width}{\code{signature(x="GenomeAxisTrack")}: the
start or end coordinates of the track items, or their width in
genomic coordinates.
-
+
\emph{Usage:}
-
+
\code{start(x)}
\code{end(x)}
\code{width(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{start(obj)}}
-
+
\item{}{\code{end(obj)}}
-
+
\item{}{\code{width(obj)}}
-
+
}
}
\item{range}{\code{signature(x="GenomeAxisTrack")}: return the genomic
coordinates for the track as an object of class
\code{\linkS4class{IRanges}}.
-
+
\emph{Usage:}
-
+
\code{range(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{range(obj)}}
}
}
-
+
\item{ranges}{\code{signature(x="GenomeAxisTrack")}: return the genomic
coordinates for the track along with all additional annotation
information as an object of class \code{\linkS4class{GRanges}}.
-
+
\emph{Usage:}
-
+
\code{ranges(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{ranges(obj)}}
}
@@ -200,13 +201,13 @@ Class \code{"\linkS4class{GdObject}"}, directly.
two.
\emph{Usage:}
-
+
\code{strand(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{strand(obj)}}
}
@@ -215,15 +216,15 @@ Class \code{"\linkS4class{GdObject}"}, directly.
\item{values}{\code{signature(x="GenomeAxisTrack")}: return all
additional annotation information except for the genomic coordinates
for the track items.
-
+
\emph{Usage:}
-
+
\code{values(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{values(obj)}}
}
@@ -231,54 +232,54 @@ Class \code{"\linkS4class{GdObject}"}, directly.
\item{subset}{\code{signature(x="GenomeAxisTrack")}: subset a
\code{GenomeAxisTrack} by coordinates and sort if necessary.
-
-
+
+
\emph{Usage:}
-
+
\code{subset(x, from, to, sort=FALSE, ...)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: the coordinates range to subset
to.}
-
+
\item{}{\code{sort}: sort the object after subsetting. Usually
not necessary.}
-
+
\item{}{\code{\dots}: additional arguments are ignored.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{subset(obj, from=10, to=20, sort=TRUE)}}
}
}
-
+
\item{length}{\code{signature(x="GenomeAxisTrack")}: return the
number of items stored in the \code{ranges} slot.
\emph{Usage:}
-
+
\code{length(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{length(obj)}}
-
+
}
}
}
-
+
\emph{Internal methods:}
-
+
\describe{
\item{drawGD}{\code{signature(GdObject="GenomeAxisTrack")}: the
@@ -288,252 +289,252 @@ Class \code{"\linkS4class{GdObject}"}, directly.
\code{drawGD(GdObject, minBase, maxBase, prepare=FALSE,
subset=TRUE, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{minBase}, \code{maxBase}: the coordinate range to
plot.}
-
+
\item{}{\code{prepare}: run method in preparation or in
production mode.}
-
+
\item{}{\code{subset}: subset the object to the visible region
or skip the potentially expensive subsetting operation.}
-
+
\item{}{\code{\dots}: all further arguments are ignored.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawGD(obj)}}
-
+
\item{}{\code{Gviz:::drawGD(obj, minBase=1, maxBase=100)}}
-
+
\item{}{\code{Gviz:::drawGD(obj, prepare=TRUE,
subset=FALSE)}}
-
+
}
}
-
+
\item{collapseTrack}{\code{signature(GdObject="GenomeAxisTrack")}:
preprocess the track before plotting. This will collapse
overlapping track items based on the available resolution and
increase the width and height of all track objects to a minimum
value to avoid rendering issues. See \code{\link{collapsing}} for
details.
-
+
\emph{Usage:}
\code{collapseTrack(GdObject, diff=.pxResolution(coord="x"))}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{diff}: the minimum pixel width to display,
everything below that will be inflated to a width of
\code{diff}.}
-
+
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::collapseTrack(obj)}}
}
}
-
+
\item{initialize}{\code{signature(.Object="GenomeAxisTrack")}:
initialize the object }
-
+
\item{show}{\code{signature(object="GenomeAxisTrack")}: show a
human-readable summary of the object }
-
+
}
\bold{\emph{Inherited:}}
-
+
\describe{
-
+
\item{displayPars}{\code{signature(x="GenomeAxisTrack", name="character")}:
list the value of the display parameter \code{name}. See
\code{\link{settings}} for details on display parameters and
customization.
-
+
\emph{Usage:}
-
+
\code{displayPars(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj, "col")}}
}
}
-
-
+
+
\item{displayPars}{\code{signature(x="GenomeAxisTrack", name="missing")}:
list the value of all available display parameters. See
\code{\link{settings}} for details on display parameters and
customization.
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj)}}
}
}
-
+
\item{getPar}{\code{signature(x="GenomeAxisTrack", name="character")}:
alias for the \code{displayPars} method. See
\code{\link{settings}} for details on display parameters and
customization.
\emph{Usage:}
-
+
\code{getPar(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj, "col")}}
}
}
-
+
\item{getPar}{\code{signature(x="GenomeAxisTrack", name="missing")}: alias
for the \code{displayPars} method. See \code{\link{settings}} for
details on display parameters and customization.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj)}}
}
}
-
+
\item{displayPars<-}{\code{signature(x="GenomeAxisTrack", value="list")}:
set display parameters using the values of the named list in
\code{value}. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{displayPars<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj) <- list(col="red", lwd=2)}}
}
}
-
+
\item{setPar}{\code{signature(x="GenomeAxisTrack", value="character")}: set
the single display parameter \code{name} to \code{value}. Note
that display parameters in the \code{GenomeAxisTrack} class are
pass-by-reference, so no re-assignmnet to the symbol \code{obj} is
necessary. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{setPar(x, name, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{name}: the name of the display parameter to set.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, "col", "red")}}
}
}
-
+
\item{setPar}{\code{signature(x="GenomeAxisTrack", value="list")}: set
display parameters by the values of the named list in
\code{value}. Note that display parameters in the \code{GenomeAxisTrack}
class are pass-by-reference, so no re-assignmnet to the symbol
\code{obj} is necessary. See \code{\link{settings}} for details on
display parameters and customization.
-
-
+
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, list(col="red", lwd=2))}}
}
}
-
+
\item{group}{\code{signature(GdObject="GenomeAxisTrack")}: return
grouping information for the individual items in the track. Unless
overwritten in one of the sub-classes, this usualy returns
\code{NULL}.
-
+
\emph{Usage:}
-
+
\code{group(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{group(obj)}}
}
}
-
+
\item{names}{\code{signature(x="GenomeAxisTrack")}: return the value of
the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj)}}
}
}
-
+
\item{names<-}{\code{signature(x="GenomeAxisTrack", value="character")}:
set the value of the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj) <- "foo"}}
}
@@ -541,15 +542,15 @@ Class \code{"\linkS4class{GdObject}"}, directly.
\item{coords}{\code{signature(ImageMap="GenomeAxisTrack")}: return the
coordinates from the internal image map.
-
+
\emph{Usage:}
-
+
\code{coords(ImageMap)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{coords(obj)}}
}
@@ -557,58 +558,58 @@ Class \code{"\linkS4class{GdObject}"}, directly.
\item{tags}{\code{signature(x="GenomeAxisTrack")}: return the tags from the
internal image map.
-
+
\emph{Usage:}
-
+
\code{tags(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{tags(obj)}}
}
}
-
+
\item{drawAxis}{\code{signature(GdObject="GenomeAxisTrack")}: add a
y-axis to the title panel of a track if necessary. Unless
overwritten in one of the sub-classes this usualy does not plot
anything and returns \code{NULL}.
-
+
\emph{Usage:}
-
+
\code{drawAxis(x, ...)}
\emph{Additional Arguments:}
-
+
\describe{
\item{}{\code{\dots}: all further arguments are ignored.}
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawAxis(obj)}}
}
}
-
+
\item{drawGrid}{\code{signature(GdObject="GenomeAxisTrack")}: superpose a
grid on top of a track if necessary. Unless overwritten in one of
the sub-classes this usualy does not plot anything and returns
\code{NULL}.
-
+
\emph{Usage:}
-
+
\code{drawGrid(GdObject, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
\item{}{\code{\dots}: additional arguments are ignored.}
@@ -616,7 +617,7 @@ Class \code{"\linkS4class{GdObject}"}, directly.
}
\emph{Examples:}
-
+
\describe{
\item{}{\code{Gviz:::drawGrid(obj)}}
@@ -627,237 +628,237 @@ Class \code{"\linkS4class{GdObject}"}, directly.
}
-\section{Display Parameters}{
+\section{Display Parameters}{
The following display parameters are set for objects of class
\code{GenomeAxisTrack} upon instantiation, unless one or more of them
have already been set by one of the optional sub-class initializers,
which always get precedence over these global defaults. See
\code{\link{settings}} for details on setting graphical parameters
- for tracks. \describe{
+ for tracks. \describe{
\item{}{\code{add35=FALSE}: Logical scalar. Add 3' to 5' direction
- indicators.}
+ indicators.}
\item{}{\code{add53=FALSE}: Logical scalar. Add 5' to 3' direction
- indicators.}
+ indicators.}
\item{}{\code{background.title="transparent"}: Character scalar.
The background color for the title panel. Defaults to omit the
- background.}
+ background.}
\item{}{\code{cex=0.8}: Numeric scalar. The overall font expansion
- factor for the axis annotation text.}
+ factor for the axis annotation text.}
\item{}{\code{cex.id=0.7}: Numeric scalar. The text size for the
- optional range annotation.}
+ optional range annotation.}
\item{}{\code{col="darkgray"}: Character scalar. The color for the
- axis lines and tickmarks.}
+ axis lines and tickmarks.}
\item{}{\code{col.border.title="transparent"}: Integer or character
- scalar. The border color for the title panels.}
+ scalar. The border color for the title panels.}
\item{}{\code{col.id="white"}: Character scalar. The text color
- for the optional range annotation.}
+ for the optional range annotation.}
\item{}{\code{col.range="cornsilk4"}: Character scalar. The border
- color for highlighted regions on the axis.}
+ color for highlighted regions on the axis.}
\item{}{\code{distFromAxis=1}: Numeric scalar. Control the distance
- of the axis annotation from the tick marks.}
+ of the axis annotation from the tick marks.}
\item{}{\code{exponent=NULL}: Numeric scalar. The exponent for the
axis coordinates, e.g., 3 means mb, 6 means gb, etc. The default
- is to automatically determine the optimal exponent.}
+ is to automatically determine the optimal exponent.}
\item{}{\code{fill.range="cornsilk3"}: Character scalar. The fill
- color for highlighted regions on the axis.}
+ color for highlighted regions on the axis.}
\item{}{\code{fontcolor="#808080"}: Character scalar. The font
- color for the axis annotation text.}
+ color for the axis annotation text.}
\item{}{\code{fontsize=10}: Numeric scalar. Font size for the axis
- annotation text in points.}
+ annotation text in points.}
\item{}{\code{labelPos="alternating"}: Character vector, one in
"alternating", "revAlternating", "above" or "below". The vertical
positioning of the axis labels. If \code{scale} is not \code{NULL},
- the possible values are "above", "below" and "beside".}
+ the possible values are "above", "below" and "beside".}
\item{}{\code{littleTicks=FALSE}: Logical scalar. Add more fine-grained
- tick marks.}
+ tick marks.}
\item{}{\code{lwd=2}: Numeric scalar. The line width for the axis
- elementes.}
+ elementes.}
\item{}{\code{lwd.border.title=1}: Integer scalar. The border width
- for the title panels.}
+ for the title panels.}
\item{}{\code{scale=NULL}: Numeric scalar. If not \code{NULL} a
small scale is drawn instead of the full axis, if the value is
between 0 and 1 it is interpreted as a fraction of the current
plotting region, otherwise as an absolute length value in genomic
- coordinates.}
+ coordinates.}
\item{}{\code{showId=FALSE}: Logical scalar. Show the optional
- range highlighting annotation.}
+ range highlighting annotation.}
\item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title panel.
- Defaults to omit the title panel.}
+ Defaults to omit the title panel.}
\item{}{\code{size=NULL}: Numeric scalar. The relative size of the
track. Can be overridden in the \code{\link{plotTracks}} function.
- Defaults to the ideal size based on the other track settings.}
+ Defaults to the ideal size based on the other track settings.}
- }
+ }
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
- plotting of \code{GenomeAxisTrack} objects.
+ plotting of \code{GenomeAxisTrack} objects.
- \describe{
+ \describe{
- \item{}{\code{\linkS4class{GdObject}}:
+ \item{}{\code{\linkS4class{GdObject}}:
- \describe{
+ \describe{
\item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ all track items.}
\item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
- for the title panel.}
+ for the title panel.}
\item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
+ character scalar. The background color of the content panel.}
\item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
factor for the axis annotation. Defaults to \code{NULL}, in
which case it is automatically determined based on the
- available space.}
+ available space.}
\item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to \code{NULL},
which means that the text size is automatically adjusted to
- the available space.}
+ the available space.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ The font and line color for the y axis, if any.}
\item{}{\code{col.frame="lightgray"}: Integer or character
scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
+ \code{col} parameter.}
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
- global \code{col} parameter.}
+ global \code{col} parameter.}
\item{}{\code{col.title="white"} \code{(Aliases: fontcolor.title)}:
- Integer or character scalar. The border color for the title panels}
+ Integer or character scalar. The border color for the title panels}
\item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
- details.}
+ details.}
\item{}{\code{fill="lightgray"}: Integer or character scalar.
Default fill color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ there is a more specific control defined elsewhere.}
\item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text, unless a more specific definition exists.}
+ font face for all text, unless a more specific definition exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
- The font face for the title panels.}
+ The font face for the title panels.}
\item{}{\code{fontfamily="sans"}: Integer or character scalar.
The font family for all text, unless a more specific definition
- exists.}
+ exists.}
\item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ scalar. The font family for the title panels.}
\item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ track when plotting.}
\item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ of a grid.}
\item{}{\code{h=-1}: Integer scalar. Parameter controlling the
number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text, unless a more specific definition exists.}
+ height for all text, unless a more specific definition exists.}
\item{}{\code{lty="solid"}: Numeric scalar. Default line type
setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
+ specific control defined elsewhere.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{lwd.title=1}: Integer scalar. The border width
- for the title panels}
+ for the title panels}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
\item{}{\code{min.height=3}: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{min.width=1}: Numeric scalar. The minimum range
width in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
plotting coordinates in 3' -> 5' direction if \code{TRUE}.
- This will effectively mirror the plot on the vertical axis.}
+ This will effectively mirror the plot on the vertical axis.}
\item{}{\code{rotation=0}: The rotation angle for all text
- unless a more specific definiton exists.}
+ unless a more specific definiton exists.}
\item{}{\code{rotation.title=90} \code{(Aliases: rotation.title)}:
The rotation angle for the text in the title panel. Even
though this can be adjusted, the automatic resizing of the
- title panel will currently not work, so use at own risk.}
+ title panel will currently not work, so use at own risk.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
- implemented).}
+ implemented).}
\item{}{\code{v=-1}: Integer scalar. Parameter controlling the
number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
- }
+ }
- }
+ }
- }
+ }
}
-
+
\author{Florian Hahne}
@@ -951,7 +952,7 @@ grTrack <- GeneRegionTrack(start=26682683, end=26711643,
rstart=cyp2b10$start, rends=cyp2b10$end, chromosome=7, genome="mm9",
transcript=cyp2b10$transcript, gene=cyp2b10$gene, symbol=cyp2b10$symbol,
name="Cyp2b10", strand=cyp2b10$strand)
-
+
plotTracks(list(grTrack, GenomeAxisTrack()))
plotTracks(list(grTrack, GenomeAxisTrack(scale=0.1)))
plotTracks(list(grTrack, GenomeAxisTrack(scale=5000)))
@@ -994,3 +995,4 @@ plotTracks(list(grTrack, GenomeAxisTrack(scale=0.5, labelPos="below")))
+
diff --git a/man/HighlightTrack-class.Rd b/man/HighlightTrack-class.Rd
index 9bb2a73..f4cfa2f 100644
--- a/man/HighlightTrack-class.Rd
+++ b/man/HighlightTrack-class.Rd
@@ -892,8 +892,6 @@ HighlightTrack(trackList=list(), range=NULL, start=NULL, end=NULL, width=NULL, c
\seealso{
- \code{\linkS4class{OverlayTrack}}
-
\code{\linkS4class{DisplayPars}}
\code{\linkS4class{GdObject}}
@@ -904,6 +902,8 @@ HighlightTrack(trackList=list(), range=NULL, start=NULL, end=NULL, width=NULL, c
\code{\linkS4class{IRanges}}
+ \code{\linkS4class{OverlayTrack}}
+
\code{\linkS4class{RangeTrack}}
\code{\link{collapsing}}
@@ -953,3 +953,4 @@ HighlightTrack(trackList=list(), range=NULL, start=NULL, end=NULL, width=NULL, c
+
diff --git a/man/IdeogramTrack-class.Rd b/man/IdeogramTrack-class.Rd
index 4feae76..6280670 100644
--- a/man/IdeogramTrack-class.Rd
+++ b/man/IdeogramTrack-class.Rd
@@ -16,6 +16,7 @@
\alias{length,IdeogramTrack-method}
\alias{[,IdeogramTrack-method}
\alias{[,IdeogramTrack,ANY,ANY-method}
+\alias{[,IdeogramTrack,ANY,ANY,ANY-method}
\alias{chromosome<-,IdeogramTrack-method}
\alias{genome<-,IdeogramTrack-method}
\alias{position,IdeogramTrack-method}
@@ -879,206 +880,206 @@ IdeogramTrack(chromosome=NULL, genome, name=NULL, bands=NULL, ...)
}
-\section{Display Parameters}{
+\section{Display Parameters}{
The following display parameters are set for objects of class
\code{IdeogramTrack} upon instantiation, unless one or more of them
have already been set by one of the optional sub-class initializers,
which always get precedence over these global defaults. See
\code{\link{settings}} for details on setting graphical parameters
- for tracks. \describe{
+ for tracks. \describe{
\item{}{\code{background.title="transparent"}: Character scalar.
The background color for the title panel. Defaults to omit the
- background.}
+ background.}
\item{}{\code{bevel=0.45}: Numeric scalar, between 0 and 1. The
- level of smoothness for the two ends of the ideogram.}
+ level of smoothness for the two ends of the ideogram.}
\item{}{\code{cex=0.8}: Numeric scalar. The overall font expansion
- factor for the chromosome name text.}
+ factor for the chromosome name text.}
\item{}{\code{cex.bands=0.7}: Numeric scalar. The font expansion
- factor for the chromosome band identifier text.}
+ factor for the chromosome band identifier text.}
\item{}{\code{col="red"}: Character scalar. The border color used
- for the highlighting of the currently displayed genomic region.}
+ for the highlighting of the currently displayed genomic region.}
\item{}{\code{col.border.title="transparent"}: Integer or character
- scalar. The border color for the title panels.}
+ scalar. The border color for the title panels.}
\item{}{\code{fill="#FFE3E6"}: Character scalar. The fill color
used for the highlighting of the currently displayed genomic
- region.}
+ region.}
\item{}{\code{fontcolor="#808080"}: Character scalar. The font
- color for the chromosome name text.}
+ color for the chromosome name text.}
\item{}{\code{fontface=1}: Character scalar. The font face for the
- chromosome name text.}
+ chromosome name text.}
\item{}{\code{fontfamily="sans"}: Character scalar. The font family
- for the chromosome name text.}
+ for the chromosome name text.}
\item{}{\code{fontsize=10}: Numeric scalar. The font size for the
- chromosome name text.}
+ chromosome name text.}
\item{}{\code{lty=1}: Character or integer scalar. The line type
used for the highlighting of the currently displayed genomic
- region.}
+ region.}
\item{}{\code{lwd=1}: Numeric scalar. The line width used for the
- highlighting of the currently displayed genomic region.}
+ highlighting of the currently displayed genomic region.}
\item{}{\code{lwd.border.title=1}: Integer scalar. The border width
- for the title panels.}
+ for the title panels.}
\item{}{\code{outline=FALSE}: Logical scalar. Add borders to the
- individual chromosome staining bands.}
+ individual chromosome staining bands.}
\item{}{\code{showBandId=FALSE}: Logical scalar. Show the identifier
- for the chromosome bands if there is space for it.}
+ for the chromosome bands if there is space for it.}
\item{}{\code{showId=TRUE}: Logical scalar. Indicate the chromosome
- name next to the ideogram.}
+ name next to the ideogram.}
\item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title panel.
- Defaults to omit the title panel.}
+ Defaults to omit the title panel.}
\item{}{\code{size=NULL}: Numeric scalar. The relative size of the
track. Defaults to automatic size setting. Can also be overridden
- in the \code{\link{plotTracks}} function.}
+ in the \code{\link{plotTracks}} function.}
- }
+ }
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
- plotting of \code{IdeogramTrack} objects.
+ plotting of \code{IdeogramTrack} objects.
- \describe{
+ \describe{
- \item{}{\code{\linkS4class{GdObject}}:
+ \item{}{\code{\linkS4class{GdObject}}:
- \describe{
+ \describe{
\item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ all track items.}
\item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
- for the title panel.}
+ for the title panel.}
\item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
+ character scalar. The background color of the content panel.}
\item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
factor for the axis annotation. Defaults to \code{NULL}, in
which case it is automatically determined based on the
- available space.}
+ available space.}
\item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to \code{NULL},
which means that the text size is automatically adjusted to
- the available space.}
+ the available space.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ The font and line color for the y axis, if any.}
\item{}{\code{col.frame="lightgray"}: Integer or character
scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
+ \code{col} parameter.}
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
- global \code{col} parameter.}
+ global \code{col} parameter.}
\item{}{\code{col.title="white"} \code{(Aliases: fontcolor.title)}:
- Integer or character scalar. The border color for the title panels}
+ Integer or character scalar. The border color for the title panels}
\item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
- details.}
+ details.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
- The font face for the title panels.}
+ The font face for the title panels.}
\item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ scalar. The font family for the title panels.}
\item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ track when plotting.}
\item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ of a grid.}
\item{}{\code{h=-1}: Integer scalar. Parameter controlling the
number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text, unless a more specific definition exists.}
+ height for all text, unless a more specific definition exists.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{lwd.title=1}: Integer scalar. The border width
- for the title panels}
+ for the title panels}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
\item{}{\code{min.height=3}: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{min.width=1}: Numeric scalar. The minimum range
width in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
plotting coordinates in 3' -> 5' direction if \code{TRUE}.
- This will effectively mirror the plot on the vertical axis.}
+ This will effectively mirror the plot on the vertical axis.}
\item{}{\code{rotation=0}: The rotation angle for all text
- unless a more specific definiton exists.}
+ unless a more specific definiton exists.}
\item{}{\code{rotation.title=90} \code{(Aliases: rotation.title)}:
The rotation angle for the text in the title panel. Even
though this can be adjusted, the automatic resizing of the
- title panel will currently not work, so use at own risk.}
+ title panel will currently not work, so use at own risk.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
- implemented).}
+ implemented).}
\item{}{\code{v=-1}: Integer scalar. Parameter controlling the
number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
- }
+ }
- }
+ }
- }
+ }
}
@@ -1089,6 +1090,8 @@ IdeogramTrack(chromosome=NULL, genome, name=NULL, bands=NULL, ...)
\code{\linkS4class{AnnotationTrack}}
+ \code{\linkS4class{data.frame}}
+
\code{\linkS4class{DisplayPars}}
\code{\linkS4class{GdObject}}
@@ -1215,3 +1218,4 @@ as(idTrack, "data.frame")
+
diff --git a/man/ImageMap-class.Rd b/man/ImageMap-class.Rd
index 78df610..0e01a62 100644
--- a/man/ImageMap-class.Rd
+++ b/man/ImageMap-class.Rd
@@ -81,3 +81,4 @@ Florian Hahne
+
diff --git a/man/NumericTrack-class.Rd b/man/NumericTrack-class.Rd
index d786c5a..8bc7d05 100644
--- a/man/NumericTrack-class.Rd
+++ b/man/NumericTrack-class.Rd
@@ -991,3 +991,4 @@
+
diff --git a/man/OverlayTrack-class.Rd b/man/OverlayTrack-class.Rd
index 2827068..23554d6 100644
--- a/man/OverlayTrack-class.Rd
+++ b/man/OverlayTrack-class.Rd
@@ -541,14 +541,14 @@ OverlayTrack(trackList=list(), name="OverlayTrack", ...)
\seealso{
- \code{\linkS4class{HighlightTrack}}
-
\code{\linkS4class{DisplayPars}}
\code{\linkS4class{GdObject}}
\code{\linkS4class{GRanges}}
+ \code{\linkS4class{HighlightTrack}}
+
\code{\linkS4class{ImageMap}}
\code{\linkS4class{IRanges}}
@@ -601,3 +601,4 @@ OverlayTrack(trackList=list(), name="OverlayTrack", ...)
+
diff --git a/man/RangeTrack-class.Rd b/man/RangeTrack-class.Rd
index bd94ee6..9d45d6b 100644
--- a/man/RangeTrack-class.Rd
+++ b/man/RangeTrack-class.Rd
@@ -6,6 +6,7 @@
\alias{[,RangeTrack-method}
\alias{[}
\alias{[,RangeTrack,ANY,ANY-method}
+\alias{[,RangeTrack,ANY,ANY,ANY-method}
\alias{chromosome,RangeTrack-method}
\alias{chromosome}
\alias{chromosome<-,RangeTrack-method}
@@ -51,19 +52,19 @@
The virtual parent class for all track items in the Gviz
package that contain some form of genomic ranges.
-
+
}
\section{Objects from the class}{
A virtual class: No objects may be created from it.
-
+
}
\section{Slots}{
\describe{
-
+
\item{\code{range}:}{Object of class \code{\linkS4class{GRanges}},
the genomic ranges of the track items as well as additional
annotation information in its \code{elementMetaData} slot. Please
@@ -71,7 +72,7 @@
\code{GRanges} and \code{\linkS4class{IRanges}} to increase
efficiency, for instance for \code{\linkS4class{DataTrack}}
objects. This usualy does not concern the user.}
-
+
\item{\code{chromosome}:}{Object of class \code{"character"}, the
chromosome on which the track is defined. There can only be a
single chromosome for one track. For certain subclasses, the space
@@ -81,118 +82,118 @@
integer scalar or as a character scalar of the form
\code{chrXYZ}, where \emph{XYZ} may be an arbitrary
character string.}
-
+
\item{\code{genome}:}{Object of class \code{"character"}, the genome
for which the track is defined. For most sub-classes this has to
be valid UCSC genome identifier, however this may not always be
formally checked upon object instantiation.}
-
+
\item{\code{dp}:}{Object of class
\code{\linkS4class{DisplayPars}}, inherited from class
\code{\linkS4class{GdObject}}.}
-
+
\item{\code{name}:}{Object of class \code{"character"}, inherited
from class \code{\linkS4class{GdObject}} }
\item{\code{imageMap}:}{Object of class
\code{\linkS4class{ImageMap}}, inherited from class
\code{\linkS4class{GdObject}}}
-
+
}
-
+
}
\section{Extends}{
-
+
Class \code{"\linkS4class{GdObject}"}, directly.
-
+
}
\section{Methods}{
-
+
In the following code chunks, \code{obj} is considered to be an object
of class \code{RangeTrack}.
-
+
\bold{\emph{Exported in the name space:}}
\describe{
-
+
\item{[}{\code{signature(x="RangeTrack", i="ANY", j="ANY",
drop="ANY")}: subset the items in the \code{RangeTrack}
object. This is essentially similar to subsetting of the
\code{\linkS4class{GRanges}} object in the \code{range}
slot. For most applications, the \code{subset} method may be
more appropriate.
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{i}, \code{j}: subsetting indices, \code{j} is
ignored.}
-
+
\item{}{\code{drop}: argument is ignored.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{obj[1:5]}}
-
+
}
}
-
-
+
+
\item{chromosome}{\code{signature(GdObject="RangeTrack")}:
return the chromosome for which the track is defined.
-
+
\emph{Usage:}
-
+
\code{chromosome(GdObject)}
\emph{Examples:}
-
+
\describe{
\item{}{\code{chromosome(obj)}}
}
}
-
+
\item{chromosome<-}{\code{signature(GdObject="RangeTrack")}:
replace the value of the track's chromosome. This has to be a
valid UCSC chromosome identifier or an integer or character
scalar that can be reasonably coerced into one.
-
+
\emph{Usage:}
-
+
\code{chromosome<-(GdObject, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
\emph{Examples:}
-
+
\describe{
\item{}{\code{chromosome(obj) <- "chr12"}}
}
}
-
+
\item{start, end, width}{\code{signature(x="RangeTrack")}: the
start or end coordinates of the track items, or their width in
genomic coordinates.
-
+
\emph{Usage:}
-
+
\code{start(x)}
\code{end(x)}
@@ -200,13 +201,13 @@
\code{width(x)}
\emph{Examples:}
-
+
\describe{
\item{}{\code{start(obj)}}
-
+
\item{}{\code{end(obj)}}
-
+
\item{}{\code{width(obj)}}
}
@@ -215,9 +216,9 @@
\item{start<-, end<-, width<-}{\code{signature(x="RangeTrack")}:
replace the start or end coordinates of the track items, or their
width.
-
+
\emph{Usage:}
-
+
\code{start<-(x, value)}
\code{end<-(x, value)}
@@ -225,63 +226,63 @@
\code{width<-(x, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
\emph{Examples:}
-
+
\describe{
\item{}{\code{start(obj) <- 1:10}}
-
+
\item{}{\code{end(obj) <- 20:30}}
-
+
\item{}{\code{width(obj) <- 1}}
}
}
-
+
\item{position}{\code{signature(GdObject="RangeTrack")}: the
arithmetic mean of the track item's coordionates, i.e.,
\code{(end(obj)-start(obj))/2}.
\emph{Usage:}
-
+
\code{position(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{position(obj)}}
}
}
-
+
\item{feature}{\code{signature(GdObject="RangeTrack")}: return the
grouping information for track items. For certain sub-classes,
groups may be indicated by different color schemes when
plotting. See \code{\link{grouping}} or
\code{\linkS4class{AnnotationTrack}} and
\code{\linkS4class{GeneRegionTrack}} for details.
-
+
\emph{Usage:}
-
+
\code{feature(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{feature(obj)}}
}
}
-
+
\item{feature<-}{\code{signature(gdObject="RangeTrack",
value="character")}: set the grouping information for track
items. This has to be a factor vector (or another type of vector
@@ -289,36 +290,36 @@
items in the \code{RangeTrack}. See \code{\link{grouping}} or
\code{\linkS4class{AnnotationTrack}} and
\code{\linkS4class{GeneRegionTrack}} for details.
-
+
\emph{Usage:}
-
+
\code{feature<-(GdObject, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{feature(obj) <- c("a", "a", "b", "c", "a")}}
}
}
-
- \item{genome}{\code{signature(x="RangeTrack")}: return the track's genome.
-
+
+ \item{genome}{\code{signature(x="RangeTrack")}: return the track's genome.
+
\emph{Usage:}
-
+
\code{genome(x)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{genome(obj)}}
@@ -329,23 +330,23 @@
\item{genome<-}{\code{signature(x="RangeTrack")}: set the track's
genome. Usually this has to be a valid UCSC identifier, however
this is not formally enforced here.
-
+
\emph{Usage:}
-
+
\code{genome<-(x, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{genome(obj) <- "mm9"}}
}
@@ -353,138 +354,138 @@
\item{length}{\code{signature(x="RangeTrack")}: return the number
of items in the track.
-
+
\emph{Usage:}
-
+
\code{length(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{length(obj)}}
}
}
-
+
\item{range}{\code{signature(x="RangeTrack")}: return the genomic
coordinates for the track as an object of class
\code{\linkS4class{IRanges}}.
-
+
\emph{Usage:}
-
+
\code{range(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{range(obj)}}
}
}
-
+
\item{ranges}{\code{signature(x="RangeTrack")}: return the genomic
coordinates for the track along with all additional annotation
information as an object of class \code{\linkS4class{GRanges}}.
-
+
\emph{Usage:}
-
+
\code{ranges(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{ranges(obj)}}
}
}
-
+
\item{split}{\code{signature(x="RangeTrack")}: split a
\code{RangeTrack} object by an appropriate factor vector (or
another vector that can be coerced into one). The output of this
operation is a list of objects of the same class as the input
object, all inheriting from class \code{RangeTrack}.
-
+
\emph{Usage:}
-
+
\code{split(x, f, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{f}: the splitting factor.}
-
+
\item{}{\code{\dots}: all further arguments are ignored.}
-
+
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{split(obj, c("a", "a", "b", "c", "a"))}}
}
}
-
+
\item{strand}{\code{signature(x="RangeTrack")}: return a vector of
strand specifiers for all track items, in the form '+' for the
Watson strand, '-' for the Crick strand or '*' for either of the
two.
-
+
\emph{Usage:}
-
+
\code{strand(x)}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{strand(obj)}}
}
}
-
+
\item{strand<-}{\code{signature(x="RangeTrack")}: replace the
strand information for the track items. The replacement value
needs to be an appropriate scalar or vector of strand values.
-
+
\emph{Usage:}
-
+
\code{strand<-(x, value)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{strand(obj) <- "+"}}
}
}
-
+
\item{values}{\code{signature(x="RangeTrack")}: return all
additional annotation information except for the genomic coordinates
for the track items as a data.frame.
-
+
\emph{Usage:}
-
+
\code{values(x)}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{values(obj)}}
}
@@ -492,37 +493,37 @@
\item{min}{\code{signature(...="RangeTrack")}:
return the start position for the leftmost range item.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{min(obj)}}
}
}
-
+
\item{max}{\code{signature(...="RangeTrack")}:
return the end position for the rightmost range item.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{max(obj)}}
}
}
-
+
\item{coerce}{\code{signature(from="RangeTrack", to="data.frame")}:
coerce the \code{\linkS4class{GRanges}} object in the
\code{range} slot into a regular data.frame.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{as(obj, "data.frame")}}
}
@@ -530,27 +531,27 @@
\item{subset}{\code{signature(x="RangeTrack")}: subset a
\code{RangeTrack} by coordinates and sort if necessary.
-
+
\emph{Usage:}
-
+
\code{subset(x, from, to, sort=FALSE, ...)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: the coordinates range to subset
to.}
-
+
\item{}{\code{sort}: sort the object after subsetting. Usually
not necessary.}
-
+
\item{}{\code{\dots}: additional arguments are ignored.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{subset(obj, from=10, to=20, sort=TRUE)}}
@@ -558,192 +559,192 @@
}
}
}
-
+
\bold{\emph{Internal methods:}}
-
+
\describe{
-
+
\item{initialize}{\code{signature(.Object="RangeTrack")}:
initialize the object. }
}
\bold{\emph{Inherited methods:}}
-
+
\describe{
\item{displayPars}{\code{signature(x="RangeTrack",
name="character")}: list the value of the display parameter
\code{name}. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{displayPars(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj, "col")}}
}
}
-
-
+
+
\item{displayPars}{\code{signature(x="RangeTrack", name="missing")}:
list the value of all available display parameters. See
\code{\link{settings}} for details on display parameters and
customization.
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj)}}
}
}
-
+
\item{getPar}{\code{signature(x="RangeTrack", name="character")}:
alias for the \code{displayPars} method. See
\code{\link{settings}} for details on display parameters and
customization.
\emph{Usage:}
-
+
\code{getPar(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj, "col")}}
}
}
-
+
\item{getPar}{\code{signature(x="RangeTrack", name="missing")}:
alias for the \code{displayPars} method. See
\code{\link{settings}} for details on display parameters and
customization.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj)}}
}
}
-
+
\item{displayPars<-}{\code{signature(x="RangeTrack", value="list")}:
set display parameters using the values of the named list in
\code{value}. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{displayPars<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj) <- list(col="red", lwd=2)}}
}
}
-
+
\item{setPar}{\code{signature(x="RangeTrack", value="character")}:
set the single display parameter \code{name} to \code{value}. Note
that display parameters in the \code{RangeTrack} class are
pass-by-reference, so no re-assignmnet to the symbol \code{obj} is
necessary. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{setPar(x, name, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{name}: the name of the display parameter to set.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, "col", "red")}}
}
}
-
+
\item{setPar}{\code{signature(x="RangeTrack", value="list")}: set
display parameters by the values of the named list in
\code{value}. Note that display parameters in the
\code{RangeTrack} class are pass-by-reference, so no re-assignmnet
to the symbol \code{obj} is necessary. See \code{\link{settings}}
for details on display parameters and customization.
-
-
+
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, list(col="red", lwd=2))}}
}
}
-
+
\item{group}{\code{signature(GdObject="RangeTrack")}: return
grouping information for the individual items in the track. Unless
overwritten in one of the sub-classes, this usualy returns
\code{NULL}.
-
+
\emph{Usage:}
-
+
\code{group(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{group(obj)}}
}
}
-
+
\item{names}{\code{signature(x="RangeTrack")}: return the value of
the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj)}}
}
}
-
+
\item{names<-}{\code{signature(x="RangeTrack", value="character")}:
set the value of the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj) <- "foo"}}
}
@@ -751,15 +752,15 @@
\item{coords}{\code{signature(ImageMap="RangeTrack")}: return the
coordinates from the internal image map.
-
+
\emph{Usage:}
-
+
\code{coords(ImageMap)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{coords(obj)}}
}
@@ -767,58 +768,58 @@
\item{tags}{\code{signature(x="RangeTrack")}: return the tags from the
internal image map.
-
+
\emph{Usage:}
-
+
\code{tags(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{tags(obj)}}
}
}
-
+
\item{drawAxis}{\code{signature(GdObject="RangeTrack")}: add a
y-axis to the title panel of a track if necessary. Unless
overwritten in one of the sub-classes this usualy does not plot
anything and returns \code{NULL}.
-
+
\emph{Usage:}
-
+
\code{drawAxis(x, ...)}
\emph{Additional Arguments:}
-
+
\describe{
\item{}{\code{\dots}: all further arguments are ignored.}
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawAxis(obj)}}
}
}
-
+
\item{drawGrid}{\code{signature(GdObject="RangeTrack")}: superpose a
grid on top of a track if necessary. Unless overwritten in one of
the sub-classes this usualy does not plot anything and returns
\code{NULL}.
-
+
\emph{Usage:}
-
+
\code{drawGrid(GdObject, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
\item{}{\code{\dots}: additional arguments are ignored.}
@@ -826,161 +827,161 @@
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawGrid(obj)}}
-
+
}
}
}
}
-\section{Display Parameters}{
+\section{Display Parameters}{
No formal display parameters are defined for objects of class
- \code{RangeTrack}.
+ \code{RangeTrack}.
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
- plotting of \code{RangeTrack} objects.
+ plotting of \code{RangeTrack} objects.
- \describe{
+ \describe{
- \item{}{\code{\linkS4class{GdObject}}:
+ \item{}{\code{\linkS4class{GdObject}}:
- \describe{
+ \describe{
\item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ all track items.}
\item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
scalar. The background color for the title panels.}
\item{}{\code{col.border.title="transparent"}: Integer or character
- scalar. The border color for the title panels.}
+ scalar. The border color for the title panels.}
\item{}{\code{lwd.border.title=1}: Integer scalar. The border
- width for the title panels.}
+ width for the title panels.}
\item{}{\code{cex=1}: Numeric scalar. The overall font expansion
- factor for all text.}
+ factor for all text.}
\item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ which case it is computed based on the available space.}
\item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to \code{NULL},
which means that the text size is automatically adjusted to
- the available space.}
+ the available space.}
\item{}{\code{col="#0080FF"}: Integer or character scalar.
Default line color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ there is a more specific control defined elsewhere.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ The font and line color for the y axis, if any.}
\item{}{\code{col.frame="lightgray"}: Integer or character
scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
+ \code{col} parameter.}
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
- global \code{col} parameter.}
+ global \code{col} parameter.}
\item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ The font color for the title panels.}
\item{}{\code{collapse=TRUE}: Boolean controlling wether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
- details.}
+ details.}
\item{}{\code{fill="lightgray"}: Integer or character scalar.
Default fill color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ there is a more specific control defined elsewhere.}
\item{}{\code{fontcolor="black"}: Integer or character scalar.
- The font color for all text.}
+ The font color for all text.}
\item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text.}
+ font face for all text.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
- The font face for the title panels.}
+ The font face for the title panels.}
\item{}{\code{fontfamily="sans"}: Integer or character scalar.
- The font family for all text.}
+ The font family for all text.}
\item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ scalar. The font family for the title panels.}
\item{}{\code{fontsize=12}: Numeric scalar. The font size for
- all text.}
+ all text.}
\item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ track when plotting.}
\item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ of a grid.}
\item{}{\code{h=-1}: Integer scalar. Parameter controlling the
number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text.}
+ height for all text.}
\item{}{\code{lty="solid"}: Numeric scalar. Default line type
setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
+ specific control defined elsewhere.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{lwd=1}: Numeric scalar. Default line width setting
for all plotting elements, unless there is a more specific
- control defined elsewhere.}
+ control defined elsewhere.}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
\item{}{\code{min.height=3}: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{min.width=1}: Numeric scalar. The minimum range
width in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
- implemented).}
+ implemented).}
\item{}{\code{showTitle=TRUE}: Boolean controlling whether to
plot a title panel. Although this can be set individually
@@ -989,21 +990,21 @@
placeholder in case any of the other tracks include a title.
The same holds true for axes. Note that the the title panel
background color could be set to transparent in order to
- completely hide it.}
+ completely hide it.}
\item{}{\code{size=1}: Numeric scalar. The relative size of
the track. Can be overridden in the \code{\link{plotTracks}}
- function.}
+ function.}
\item{}{\code{v=-1}: Integer scalar. Parameter controlling the
number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
- }
+ }
- }
+ }
- }
+ }
}
@@ -1073,3 +1074,4 @@
+
diff --git a/man/ReferenceTrack-class.Rd b/man/ReferenceTrack-class.Rd
index efebd5a..9b0256e 100644
--- a/man/ReferenceTrack-class.Rd
+++ b/man/ReferenceTrack-class.Rd
@@ -148,3 +148,4 @@ availableDefaultMapping(file, trackType)
+
diff --git a/man/SequenceTrack-class.Rd b/man/SequenceTrack-class.Rd
index dfd02d8..af49203 100644
--- a/man/SequenceTrack-class.Rd
+++ b/man/SequenceTrack-class.Rd
@@ -809,10 +809,16 @@ importFunction, stream=FALSE, ...)
\code{\linkS4class{AnnotationTrack}}
+ \code{\linkS4class{BSgenome}}
+
\code{\linkS4class{DataTrack}}
\code{\linkS4class{DisplayPars}}
+ \code{\linkS4class{DNAString}}
+
+ \code{\linkS4class{DNAStringSet}}
+
\code{\linkS4class{GdObject}}
\code{\linkS4class{GeneRegionTrack}}
@@ -823,9 +829,9 @@ importFunction, stream=FALSE, ...)
\code{\linkS4class{IRanges}}
- \code{\linkS4class{BSgenome}}
+ \code{\link{collapsing}}
- \code{\linkS4class{DNAStringSet}}
+ \code{\link{panel.grid}}
\code{\link{plotTracks}}
@@ -939,3 +945,4 @@ subseq(sTrack, start=length(sTrack), width=20)
+
diff --git a/man/StackedTrack-class.Rd b/man/StackedTrack-class.Rd
index 71e3d2f..1375c56 100644
--- a/man/StackedTrack-class.Rd
+++ b/man/StackedTrack-class.Rd
@@ -14,12 +14,13 @@
\alias{stacks}
\alias{subset,StackedTrack-method}
\alias{[,StackedTrack,ANY,ANY-method}
+\alias{[,StackedTrack,ANY,ANY,ANY-method}
\alias{consolidateTrack,StackedTrack-method}
\title{StackedTrack class and methods}
\description{
-
+
The virtual parent class for all track types in the Gviz
package which contain potentially overlapping annotation items that
have to be stacked when plotted.
@@ -29,20 +30,20 @@
\section{Objects from the Class}{
A virtual Class: No objects may be created from it.
-
+
}
\section{Slots}{
-
+
\describe{
-
+
\item{\code{stacking}:}{Object of class \code{"character"}, the
stacking type of overlapping items on the final plot. One in
\code{c(hide, dense, squish, pack,full)}. Currently, only
\code{hide} (do not show the track items at all), \code{squish}
(make best use of the available space) and \code{dense} (no
stacking at all) are implemented. }
-
+
\item{\code{stacks}:}{Object of class \code{"numeric"}, holding the
stack indices for each track item. This slot is usually populated
by calling the \code{setStacks} method upon plotting, since the
@@ -67,61 +68,61 @@
\item{\code{imageMap}:}{Object of class \code{\linkS4class{ImageMap}},
inherited from class \code{\linkS4class{GdObject}}}
-
+
}
}
\section{Extends}{
-
+
Class \code{"\linkS4class{RangeTrack}"}, directly.
-
+
Class \code{"\linkS4class{GdObject}"}, by class "RangeTrack", distance 2.
-
+
}
\section{Methods}{
In the following code chunks, \code{obj} is considered to be an object
of class \code{StackedTrack}.
-
+
\bold{\emph{Exported in the name space:}}
\describe{
-
+
\item{stacking}{\code{signature(GdObject="StackedTrack")}: return
the current stacking type.
-
+
\emph{Usage:}
-
+
\code{stacking(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{stacking(obj)}}
}
}
-
+
\item{stacking<-}{\code{signature(GdObject="StackedTrack",
value="character")}: set the object's stacking type to one in
\code{c(hide, dense, squish, pack,full)}.
-
+
\emph{Usage:}
-
+
\code{stacking<-(GdObject, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
\emph{Examples:}
-
+
\describe{
\item{}{\code{stacking(obj) <- "squish" }}
@@ -129,7 +130,7 @@
}
}
}
-
+
\bold{\emph{Internal methods:}}
\describe{
@@ -144,166 +145,166 @@
graphical output is created. Note that the method for this
particular subclass is usually called through inheritance and not
particularly useful on its own.
-
+
\emph{Usage:}
\code{drawGD(GdObject, minBase, maxBase, prepare=FALSE,
subset=TRUE, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{minBase}, \code{maxBase}: the coordinate range to
plot.}
-
+
\item{}{\code{prepare}: run method in preparation or in
production mode.}
-
+
\item{}{\code{subset}: subset the object to the visible region
or skip the potentially expensive subsetting operation.}
-
+
\item{}{\code{\dots}: all further arguments are ignored.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::drawGD(obj, prepare=FALSE)}}
-
+
}
}
\item{setStacks}{\code{signature(GdObject="StackedTrack")}:
recompute the stacks based on the available space and on the
object's track items and stacking settings.
-
+
\emph{Usage:}
-
+
\code{setStacks(GdObject, from, to)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: compute stacking within a
certain coordinates range. This needs to be supplied for the
plotting function to know the current genomic coordinates.}
-
+
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::setStacks(obj)}}
}
}
-
+
\item{stacks}{\code{signature(GdObject="StackedTrack")}: return
the stack indices for each track item.
\emph{Usage:}
-
+
\code{stacks(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{Gviz:::stacks(obj)}}
}
}
-
+
\item{initialize}{\code{signature(.Object="StackedTrack")}:
initialize the object. }
-
+
}
\bold{\emph{Inherited methods:}}
-
+
\describe{
-
+
\item{[}{\code{signature(x="StackedTrack", i="ANY", j="ANY",
drop="ANY")}: subset the items in the \code{StackedTrack}
object. This is essentially similar to subsetting of the
\code{\linkS4class{GRanges}} object in the \code{range}
slot. For most applications, the \code{subset} method may be
more appropriate.
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{i}, \code{j}: subsetting indices, \code{j} is
ignored.}
-
+
\item{}{\code{drop}: argument is ignored.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{obj[1:5]}}
-
+
}
}
-
-
+
+
\item{chromosome}{\code{signature(GdObject="StackedTrack")}:
return the chromosome for which the track is defined.
-
+
\emph{Usage:}
-
+
\code{chromosome(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{chromosome(obj)}}
-
+
}
}
-
+
\item{chromosome<-}{\code{signature(GdObject="StackedTrack")}:
replace the value of the track's chromosome. This has to be a
valid UCSC chromosome identifier or an integer or character
scalar that can be reasonably coerced into one.
-
+
\emph{Usage:}
-
+
\code{chromosome<-(GdObject, value)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{chromosome(obj) <- "chr12"}}
-
+
}
}
-
+
\item{start, end, width}{\code{signature(x="StackedTrack")}: the
start or end coordinates of the track items, or their width in
genomic coordinates.
-
+
\emph{Usage:}
-
+
\code{start(x)}
\code{end(x)}
@@ -311,13 +312,13 @@
\code{width(x)}
\emph{Examples:}
-
+
\describe{
\item{}{\code{start(obj)}}
-
+
\item{}{\code{end(obj)}}
-
+
\item{}{\code{width(obj)}}
}
@@ -326,9 +327,9 @@
\item{start<-, end<-, width<-}{\code{signature(x="StackedTrack")}:
replace the start or end coordinates of the track items, or their
width.
-
+
\emph{Usage:}
-
+
\code{start<-(x, value)}
\code{end<-(x, value)}
@@ -336,63 +337,63 @@
\code{width<-(x, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
\emph{Examples:}
-
+
\describe{
\item{}{\code{start(obj) <- 1:10}}
-
+
\item{}{\code{end(obj) <- 20:30}}
-
+
\item{}{\code{width(obj) <- 1}}
}
}
-
+
\item{position}{\code{signature(GdObject="StackedTrack")}: the
arithmetic mean of the track item's coordionates, i.e.,
\code{(end(obj)-start(obj))/2}.
\emph{Usage:}
-
+
\code{position(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{position(obj)}}
}
}
-
+
\item{feature}{\code{signature(GdObject="StackedTrack")}: return the
grouping information for track items. For certain sub-classes,
groups may be indicated by different color schemes when
plotting. See \code{\link{grouping}} or
\code{\linkS4class{AnnotationTrack}} and
\code{\linkS4class{GeneRegionTrack}} for details.
-
+
\emph{Usage:}
-
+
\code{feature(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{feature(obj)}}
}
}
-
+
\item{feature<-}{\code{signature(gdObject="StackedTrack",
value="character")}: set the grouping information for track
items. This has to be a factor vector (or another type of vector
@@ -400,36 +401,36 @@
items in the \code{StackedTrack}. See \code{\link{grouping}} or
\code{\linkS4class{AnnotationTrack}} and
\code{\linkS4class{GeneRegionTrack}} for details.
-
+
\emph{Usage:}
-
+
\code{feature<-(GdObject, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{feature(obj) <- c("a", "a", "b", "c", "a")}}
}
}
-
- \item{genome}{\code{signature(x="StackedTrack")}: return the track's genome.
-
+
+ \item{genome}{\code{signature(x="StackedTrack")}: return the track's genome.
+
\emph{Usage:}
-
+
\code{genome(x)}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{genome(obj)}}
@@ -440,23 +441,23 @@
\item{genome<-}{\code{signature(x="StackedTrack")}: set the track's
genome. Usually this has to be a valid UCSC identifier, however
this is not formally enforced here.
-
+
\emph{Usage:}
-
+
\code{genome<-(x, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{genome(obj) <- "mm9"}}
}
@@ -464,151 +465,151 @@
\item{length}{\code{signature(x="StackedTrack")}: return the number
of items in the track.
-
+
\emph{Usage:}
-
+
\code{length(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{length(obj)}}
}
}
-
+
\item{range}{\code{signature(x="StackedTrack")}: return the genomic
coordinates for the track as an object of class
\code{\linkS4class{IRanges}}.
-
+
\emph{Usage:}
-
+
\code{range(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{range(obj)}}
}
}
-
+
\item{ranges}{\code{signature(x="StackedTrack")}: return the genomic
coordinates for the track along with all additional annotation
information as an object of class \code{\linkS4class{GRanges}}.
-
+
\emph{Usage:}
-
+
\code{ranges(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{ranges(obj)}}
}
}
-
+
\item{split}{\code{signature(x="StackedTrack")}: split a
\code{StackedTrack} object by an appropriate factor vector (or
another vector that can be coerced into one). The output of this
operation is a list of objects of the same class as the input
object, all inheriting from class \code{StackedTrack}.
-
+
\emph{Usage:}
-
+
\code{split(x, f, ...)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{f}: the splitting factor.}
-
+
\item{}{\code{\dots}: all further arguments are ignored.}
-
+
}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{split(obj, c("a", "a", "b", "c", "a"))}}
}
}
-
+
\item{strand}{\code{signature(x="StackedTrack")}: return a vector of
strand specifiers for all track items, in the form '+' for the
Watson strand, '-' for the Crick strand or '*' for either of the
two.
-
+
\emph{Usage:}
-
+
\code{strand(x)}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{strand(obj)}}
}
}
-
+
\item{strand<-}{\code{signature(x="StackedTrack")}: replace the
strand information for the track items. The replacement value
needs to be an appropriate scalar or vector of strand values.
-
+
\emph{Usage:}
-
+
\code{strand<-(x, value)}
-
+
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{value}: replacement value.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{strand(obj) <- "+"}}
}
}
-
+
\item{values}{\code{signature(x="StackedTrack")}: return all
additional annotation information except for the genomic coordinates
for the track items as a data.frame.
-
+
\emph{Usage:}
-
+
\code{values(x)}
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{values(obj)}}
}
}
-
+
\item{coerce}{\code{signature(from="StackedTrack",
to="data.frame")}: coerce the \code{\linkS4class{GRanges}}
object in the \code{range} slot into a regular data.frame.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{as(obj, "data.frame")}}
}
@@ -616,145 +617,145 @@
\item{subset}{\code{signature(x="StackedTrack")}: subset a
\code{StackedTrack} by coordinates and sort if necessary.
-
+
\emph{Usage:}
-
+
\code{subset(x, from, to, sort=FALSE, ...)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{from}, \code{to}: the coordinates range to subset
to.}
-
+
\item{}{\code{sort}: sort the object after subsetting. Usually
not necessary.}
-
+
\item{}{\code{\dots}: additional arguments are ignored.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
\item{}{\code{subset(obj, from=10, to=20, sort=TRUE)}}
}
}
-
+
\item{displayPars}{\code{signature(x="StackedTrack",
name="character")}: list the value of the display parameter
\code{name}. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{displayPars(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj, "col")}}
-
+
}
}
-
-
+
+
\item{displayPars}{\code{signature(x="StackedTrack",
name="missing")}: list the value of all available display
parameters. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj)}}
}
}
-
+
\item{getPar}{\code{signature(x="StackedTrack", name="character")}:
alias for the \code{displayPars} method. See
\code{\link{settings}} for details on display parameters and
customization.
\emph{Usage:}
-
+
\code{getPar(x, name)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj, "col")}}
}
}
-
+
\item{getPar}{\code{signature(x="StackedTrack", name="missing")}:
alias for the \code{displayPars} method. See
\code{\link{settings}} for details on display parameters and
customization.
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{getPar(obj)}}
}
}
-
+
\item{displayPars<-}{\code{signature(x="StackedTrack",
value="list")}: set display parameters using the values of the
named list in \code{value}. See \code{\link{settings}} for details
on display parameters and customization.
-
+
\emph{Usage:}
-
+
\code{displayPars<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{displayPars(obj) <- list(col="red", lwd=2)}}
}
}
-
+
\item{setPar}{\code{signature(x="StackedTrack", value="character")}:
set the single display parameter \code{name} to \code{value}. Note
that display parameters in the \code{StackedTrack} class are
pass-by-reference, so no re-assignmnet to the symbol \code{obj} is
necessary. See \code{\link{settings}} for details on display
parameters and customization.
-
+
\emph{Usage:}
-
+
\code{setPar(x, name, value)}
\emph{Additional Arguments:}
-
+
\describe{
-
+
\item{}{\code{name}: the name of the display parameter to set.}
-
+
}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, "col", "red")}}
}
}
-
+
\item{setPar}{\code{signature(x="StackedTrack", value="list")}: set
display parameters by the values of the named list in
\code{value}. Note that display parameters in the
@@ -762,62 +763,62 @@
re-assignmnet to the symbol \code{obj} is necessary. See
\code{\link{settings}} for details on display parameters and
customization.
-
-
+
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{setPar(obj, list(col="red", lwd=2))}}
}
}
-
+
\item{group}{\code{signature(GdObject="StackedTrack")}: return
grouping information for the individual items in the track. Unless
overwritten in one of the sub-classes, this usualy returns
\code{NULL}.
-
+
\emph{Usage:}
-
+
\code{group(GdObject)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{group(obj)}}
}
}
-
+
\item{names}{\code{signature(x="StackedTrack")}: return the value of
the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj)}}
}
}
-
+
\item{names<-}{\code{signature(x="StackedTrack", value="character")}:
set the value of the \code{name} slot.
-
+
\emph{Usage:}
-
+
\code{names<-(x, value)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{names(obj) <- "foo"}}
}
@@ -825,15 +826,15 @@
\item{coords}{\code{signature(ImageMap="StackedTrack")}: return the
coordinates from the internal image map.
-
+
\emph{Usage:}
-
+
\code{coords(ImageMap)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{coords(obj)}}
}
@@ -841,15 +842,15 @@
\item{tags}{\code{signature(x="StackedTrack")}: return the tags from the
internal image map.
-
+
\emph{Usage:}
-
+
\code{tags(x)}
-
+
\emph{Examples:}
-
+
\describe{
-
+
\item{}{\code{tags(obj)}}
}
@@ -867,7 +868,7 @@
\code{\link{settings}} for details on setting graphical parameters
for tracks.
- \describe{
+ \describe{
\item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse the
y-ordering of stacked items. I.e., features that are plotted on
@@ -887,143 +888,143 @@
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
- plotting of \code{StackedTrack} objects.
+ plotting of \code{StackedTrack} objects.
- \describe{
+ \describe{
- \item{}{\code{\linkS4class{GdObject}}:
+ \item{}{\code{\linkS4class{GdObject}}:
- \describe{
+ \describe{
\item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ all track items.}
\item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panels.}
+ scalar. The background color for the title panels.}
\item{}{\code{col.border.title="transparent"}: Integer or character
- scalar. The border color for the title panels.}
+ scalar. The border color for the title panels.}
\item{}{\code{lwd.border.title=1}: Integer scalar. The border
width for the title panels.}
\item{}{\code{cex=1}: Numeric scalar. The overall font expansion
- factor for all text.}
+ factor for all text.}
\item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ which case it is computed based on the available space.}
\item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to \code{NULL},
which means that the text size is automatically adjusted to
- the available space.}
+ the available space.}
\item{}{\code{col="#0080FF"}: Integer or character scalar.
Default line color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ there is a more specific control defined elsewhere.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ The font and line color for the y axis, if any.}
\item{}{\code{col.frame="lightgray"}: Integer or character
scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
+ \code{col} parameter.}
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
- global \code{col} parameter.}
+ global \code{col} parameter.}
\item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ The font color for the title panels.}
\item{}{\code{collapse=TRUE}: Boolean controlling wether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
- details.}
+ details.}
\item{}{\code{fill="lightgray"}: Integer or character scalar.
Default fill color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ there is a more specific control defined elsewhere.}
\item{}{\code{fontcolor="black"}: Integer or character scalar.
- The font color for all text.}
+ The font color for all text.}
\item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text.}
+ font face for all text.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
- The font face for the title panels.}
+ The font face for the title panels.}
\item{}{\code{fontfamily="sans"}: Integer or character scalar.
- The font family for all text.}
+ The font family for all text.}
\item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ scalar. The font family for the title panels.}
\item{}{\code{fontsize=12}: Numeric scalar. The font size for
- all text.}
+ all text.}
\item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ track when plotting.}
\item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ of a grid.}
\item{}{\code{h=-1}: Integer scalar. Parameter controlling the
number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text.}
+ height for all text.}
\item{}{\code{lty="solid"}: Numeric scalar. Default line type
setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
+ specific control defined elsewhere.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \code{grid==TRUE}.}
\item{}{\code{lwd=1}: Numeric scalar. Default line width setting
for all plotting elements, unless there is a more specific
- control defined elsewhere.}
+ control defined elsewhere.}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
\item{}{\code{min.height=3}: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{min.width=1}: Numeric scalar. The minimum range
width in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ for details.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
- implemented).}
+ implemented).}
\item{}{\code{showTitle=TRUE}: Boolean controlling whether to
plot a title panel. Although this can be set individually
@@ -1032,21 +1033,21 @@
placeholder in case any of the other tracks include a title.
The same holds true for axes. Note that the the title panel
background color could be set to transparent in order to
- completely hide it.}
+ completely hide it.}
\item{}{\code{size=1}: Numeric scalar. The relative size of
the track. Can be overridden in the \code{\link{plotTracks}}
- function.}
+ function.}
\item{}{\code{v=-1}: Integer scalar. Parameter controlling the
number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ for details.}
- }
+ }
- }
+ }
- }
+ }
}
@@ -1118,3 +1119,4 @@
+
diff --git a/man/UcscTrack.Rd b/man/UcscTrack.Rd
index 2e3f51a..d56569f 100644
--- a/man/UcscTrack.Rd
+++ b/man/UcscTrack.Rd
@@ -135,3 +135,4 @@ Florian Hahne
+
diff --git a/man/collapsing.Rd b/man/collapsing.Rd
index e837100..311f232 100644
--- a/man/collapsing.Rd
+++ b/man/collapsing.Rd
@@ -55,3 +55,4 @@
+
diff --git a/man/datasets.Rd b/man/datasets.Rd
index 84daea7..e74e7b6 100644
--- a/man/datasets.Rd
+++ b/man/datasets.Rd
@@ -38,3 +38,4 @@ Some sample data sets used for the illustrative examples and the vignette.
+
diff --git a/man/exportTracks.Rd b/man/exportTracks.Rd
index 25841c3..b4ef3d7 100644
--- a/man/exportTracks.Rd
+++ b/man/exportTracks.Rd
@@ -52,3 +52,4 @@ FIXME: Need to support wgl exports as well...
+
diff --git a/man/grouping.Rd b/man/grouping.Rd
index 62f45ca..c138832 100644
--- a/man/grouping.Rd
+++ b/man/grouping.Rd
@@ -46,3 +46,4 @@
+
diff --git a/man/plotTracks.Rd b/man/plotTracks.Rd
index c5c069f..9205f30 100644
--- a/man/plotTracks.Rd
+++ b/man/plotTracks.Rd
@@ -207,3 +207,4 @@ scales=list(x="free"))
+
diff --git a/man/settings.Rd b/man/settings.Rd
index 6dc469f..3570b94 100644
--- a/man/settings.Rd
+++ b/man/settings.Rd
@@ -125,64 +125,78 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{cex.id=0.7}: Numeric scalar. The text size for
- the optional range annotation.}
+ \item{}{\code{add35=FALSE}: Logical scalar. Add 3' to 5'
+ direction indicators.}
- \item{}{\code{fontsize=10}: Numeric scalar. Font size for the
- axis annotation text in points.}
+ \item{}{\code{add53=FALSE}: Logical scalar. Add 5' to 3'
+ direction indicators.}
\item{}{\code{background.title="transparent"}: Character scalar.
The background color for the title panel. Defaults to omit
the background.}
- \item{}{\code{fontcolor="#808080"}: Character scalar. The font
- color for the axis annotation text.}
-
- \item{}{\code{size=NULL}: Numeric scalar. The relative size of
- the track. Can be overridden in the \code{\link{plotTracks}}
- function. Defaults to the ideal size based on the other track
- settings.}
+ \item{}{\code{cex.id=0.7}: Numeric scalar. The text size for
+ the optional range annotation.}
- \item{}{\code{lwd=2}: Numeric scalar. The line width for the
- axis elementes.}
+ \item{}{\code{cex=0.8}: Numeric scalar. The overall font
+ expansion factor for the axis annotation text.}
- \item{}{\code{add35=FALSE}: Logical scalar. Add 3' to 5'
- direction indicators.}
+ \item{}{\code{col.border.title="transparent"}: Integer or
+ character scalar. The border color for the title panels.}
- \item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title
- panel. Defaults to omit the title panel.}
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
- \item{}{\code{add53=FALSE}: Logical scalar. Add 5' to 3'
- direction indicators.}
+ \item{}{\code{col.id="white"}: Character scalar. The text color
+ for the optional range annotation.}
- \item{}{\code{littleTicks=FALSE}: Logical scalar. Add more
- fine-grained tick marks.}
+ \item{}{\code{col.range="cornsilk4"}: Character scalar. The
+ border color for highlighted regions on the axis.}
\item{}{\code{distFromAxis=1}: Numeric scalar. Control the
distance of the axis annotation from the tick marks.}
- \item{}{\code{col.id="white"}: Character scalar. The text color
- for the optional range annotation.}
-
- \item{}{\code{labelPos="alternating"}: Character vector, one
- in "alternating", "revAlternating", "above" or "below". The
- vertical positioning of the axis labels.}
-
\item{}{\code{exponent=NULL}: Numeric scalar. The exponent for
the axis coordinates, e.g., 3 means mb, 6 means gb, etc. The
default is to automatically determine the optimal exponent.}
- \item{}{\code{cex=0.8}: Numeric scalar. The overall font
- expansion factor for the axis annotation text.}
-
\item{}{\code{fill.range="cornsilk3"}: Character scalar. The
fill color for highlighted regions on the axis.}
+ \item{}{\code{fontcolor="#808080"}: Character scalar. The font
+ color for the axis annotation text.}
+
+ \item{}{\code{fontsize=10}: Numeric scalar. Font size for the
+ axis annotation text in points.}
+
+ \item{}{\code{labelPos="alternating"}: Character vector, one
+ in "alternating", "revAlternating", "above" or "below". The
+ vertical positioning of the axis labels. If \code{scale} is
+ not \code{NULL}, the possible values are "above", "below"
+ and "beside".}
+
+ \item{}{\code{littleTicks=FALSE}: Logical scalar. Add more
+ fine-grained tick marks.}
+
+ \item{}{\code{lwd=2}: Numeric scalar. The line width for the
+ axis elementes.}
+
+ \item{}{\code{scale=NULL}: Numeric scalar. If not \code{NULL}
+ a small scale is drawn instead of the full axis, if the value
+ is between 0 and 1 it is interpreted as a fraction of the
+ current plotting region, otherwise as an absolute length
+ value in genomic coordinates.}
+
\item{}{\code{showId=FALSE}: Logical scalar. Show the optional
range highlighting annotation.}
- \item{}{\code{col.range="cornsilk4"}: Character scalar. The
- border color for highlighted regions on the axis.}
+ \item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title
+ panel. Defaults to omit the title panel.}
+
+ \item{}{\code{size=NULL}: Numeric scalar. The relative size of
+ the track. Can be overridden in the \code{\link{plotTracks}}
+ function. Defaults to the ideal size based on the other track
+ settings.}
\item{}{\code{col="darkgray"}: Character scalar. The color for
the axis lines and tickmarks.}
@@ -193,113 +207,133 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text.}
+ \item{}{\code{alpha=1}: Numeric scalar. The transparency for
+ all track items.}
- \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
- number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
- \item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ \item{}{\code{background.panel="transparent"}: Integer or
+ character scalar. The background color of the content panel.}
- \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
+ factor for the axis annotation. Defaults to \code{NULL}, in
+ which case it is automatically determined based on the
+ available space.}
- \item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
+ factor for the title panel. This effects the fontsize of both
+ the title and the axis, if any. Defaults to \code{NULL},
+ which means that the text size is automatically adjusted to
+ the available space.}
- \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ \item{}{\code{col.axis="white"}: Integer or character scalar.
+ The font and line color for the y axis, if any.}
- \item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ \item{}{\code{col.frame="lightgray"}: Integer or character
+ scalar. The line color used for the panel frame, if
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{lty="solid"}: Numeric scalar. Default line type
- setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
-
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
\code{col} parameter.}
- \item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
-
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global \code{col} parameter.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
-
- \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
- number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{col.title="white"}: Integer or character scalar.
+ The border color for the title panels}
- \item{}{\code{collapse=TRUE}: Boolean controlling wether to
+ \item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
details.}
- \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
- factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ \item{}{\code{fill="lightgray"}: Integer or character scalar.
+ Default fill color setting for all plotting elements, unless
+ there is a more specific control defined elsewhere.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
The font face for the title panels.}
- \item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text.}
+ \item{}{\code{fontface=1}: Integer or character scalar. The
+ font face for all text, unless a more specific definition exists.}
- \item{}{\code{fill="lightgray"}: Integer or character scalar.
- Default fill color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ \item{}{\code{fontfamily.title="sans"}: Integer or character
+ scalar. The font family for the title panels.}
- \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
- for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ \item{}{\code{fontfamily="sans"}: Integer or character scalar.
+ The font family for all text, unless a more specific definition
+ exists.}
- \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
- factor for the title panel. This effects the fontsize of both
- the title and the axis, if any. Defaults to \code{NULL},
- which means that the text size is automatically adjusted to
- the available space.}
+ \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
+ track when plotting.}
- \item{}{\code{col.frame="lightgray"}: Integer or character
- scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
+ of a grid.}
- \item{}{\code{min.height=3}: Numeric scalar. The minimum range
- height in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
+ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
+ number of horizontal grid lines, see \code{\link{panel.grid}}
for details.}
+ \item{}{\code{lineheight=1}: Numeric scalar. The font line
+ height for all text, unless a more specific definition exists.}
+
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{lty="solid"}: Numeric scalar. Default line type
+ setting for all plotting elements, unless there is a more
+ specific control defined elsewhere.}
+
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
+
+ \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
+ for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
\code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \item{}{\code{min.height=3}: Numeric scalar. The minimum range
+ height in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
+
+ \item{}{\code{rotation.title=90}: The rotation angle for the
+ text in the title panel. Even though this can be adjusted,
+ the automatic resizing of the title panel will currently not
+ work, so use at own risk.}
+
+ \item{}{\code{rotation=0}: The rotation angle for all text
+ unless a more specific definiton exists.}
+
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).}
- \item{}{\code{fontfamily="sans"}: Integer or character scalar.
- The font family for all text.}
+ \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
+ number of vertical grid lines, see \code{\link{panel.grid}}
+ for details.}
}
@@ -309,118 +343,157 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{pch=20}: Integer scalar. The type of glyph used
- for plotting symbols.}
+ \item{}{\code{aggregateGroups=FALSE}: Logical scalar. Aggregate
+ the values within a sample group using the aggregation
+ funnction specified in the \code{aggregation} parameter.}
- \item{}{\code{notch=FALSE}: Logical scalar. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ \item{}{\code{aggregation="mean"}: Function or character scalar.
+ Used to aggregate values in windows or for collapsing
+ overlapping items. The function has to accept a numeric vector
+ as a single input parameter and has to return a numeric scalar
+ with the aggregated value. Alternatively, one of the predefined
+ options \code{mean}, \code{median} \code{sum}, \code{min},
+ \code{max} or \code{extreme} can be supplied as a character
+ scalar. Defaults to \code{mean}.}
- \item{}{\code{cex=0.7}: Numeric scalar. The default pixel size
- for plotting symbols.}
+ \item{}{\code{alpha.confint=0.3}: Numeric scalar. The transparency
+ for the confidence intervalls in confint-type plots.}
+
+ \item{}{\code{amount=NULL}: Numeric scalar. Amount of jittering
+ in xy-type plots. See \code{\link{panel.xyplot}} for details.}
+
+ \item{}{\code{baseline=NULL}: Numeric scalar. Y-axis position
+ of an optional baseline. This parameter has a special meaning
+ for mountain-type and polygon-type plots, see the 'Details'
+ section in \code{\linkS4class{DataTrack}} for more information.}
+
+ \item{}{\code{box.legend=FALSE}: Logical scalar. Draw a box
+ around a legend.}
+
+ \item{}{\code{box.ratio=1}: Numeric scalar. Parameter controlling
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
\item{}{\code{box.width=NULL}: Numeric scalar. Parameter
controlling the boxplot appearance. See \code{\link{panel.bwplot}}
for details.}
- \item{}{\code{stackedBars=TRUE}: Logical scalar. When there
- are several data groups, draw the histogram-type plots as
- stacked barplots or grouped side by side.}
+ \item{}{\code{grid=FALSE}: Logical vector. Draw a line grid
+ under the track content.}
- \item{}{\code{levels.fos=NULL}: Numeric scalar. Parameter
- controlling the boxplot appearance. See \code{\link{panel.bwplot}}
- for details.}
+ \item{}{\code{cex.legend=0.8}: Numeric scalar. The size factor
+ for the legend text.}
- \item{}{\code{gradient=c("#F7FBFF", "#DEEBF7", "#C6DBEF",
- "#9ECAE1", "#6BAED6", "#4292C6", "#2171B5", "#08519C",
- "#08306B")}: Character vector. The base colors for the
- 'gradient' plotting type.}
+ \item{}{\code{cex.sampleNames=NULL}: Numeric scalar. The size
+ factor for the sample names text in heatmap or horizon plots.
+ Defaults to an automatic setting.}
- \item{}{\code{min.distance=0}: Numeric scalar. The mimimum
- distance in pixel below which to collapse ranges.}
+ \item{}{\code{cex=0.7}: Numeric scalar. The default pixel size
+ for plotting symbols.}
- \item{}{\code{degree=1}: Numeric scalar. Parameter controlling
- the loess calculation for smooth and mountain-type plots.
- See \code{\link{panel.loess}} for details.}
+ \item{}{\code{coef=1.5}: Numeric scalar. Parameter controlling
+ the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
- \item{}{\code{type="p"}: Character vector. The plot type, one
- or several in \code{c("p","l", "b", "a", "s", "g", "r", "S",
- "smooth", "histogram", "mountain", "h", "boxplot", "gradient",
- "heatmap")}. See 'Details' section in \code{\linkS4class{DataTrack}}
- for more information on the individual plotting types.}
+ \item{}{\code{col.baseline=NULL}: Character scalar. Color for
+ the optional baseline, defaults to the setting of \code{col}.}
- \item{}{\code{notch.frac=0.5}: Numeric scalar. Parameter
- controlling the boxplot appearance. See \code{\link{panel.bwplot}}
+ \item{}{\code{col.confint=NA}: Character vector. Border colors
+ for the confidence intervals for confint-type plots.}
+
+ \item{}{\code{col.histogram="#808080"}: Character scalar. Line
+ color in histogram-type plots.}
+
+ \item{}{\code{col.horizon=NA}: The line color for the segments
+ in the \code{horizon}-type plot. See \code{\link{horizonplot}}
for details.}
- \item{}{\code{ylim=NULL}: Numeric vector of length 2. The range
- of the y-axis scale.}
+ \item{}{\code{col.mountain=NULL}: Character scalar. Line color
+ in mountain-type and polygon-type plots, defaults to the
+ setting of \code{col}.}
- \item{}{\code{fill.histogram="lightgray"}: Character scalar.
- Fill color in histogram-type plots, defaults to the setting
- of \code{fill}.}
+ \item{}{\code{col.sampleNames="white"}: Character or integer
+ scalar. The color used for the sample names in heatmap plots.}
- \item{}{\code{baseline=NULL}: Numeric scalar. Y-axis position
- of an optional baseline. This parameter has a special meaning
- for mountain-type plots, see the 'Details' section in
- \code{\linkS4class{DataTrack}} for more information.}
+ \item{}{\code{col=c("#0080ff", "#ff00ff", "darkgreen", "#ff0000",
+ "orange", "#00ff00", "brown")}: Character or integer vector.
+ The color used for all line and symbol elements, unless there
+ is a more specific control defined elsewhere. Unless
+ \code{groups} are specified, only the first color in the
+ vector is usually regarded.}
\item{}{\code{collapse=FALSE}: Logical scalar. Collapse
overlapping ranges and aggregate the underlying data.}
- \item{}{\code{size=NULL}: Numeric scalar. The relative size of
- the track. Can be overridden in the \code{\link{plotTracks}}
- function. By default the size will be set automatically based
- on the selected plotting type.}
-
- \item{}{\code{col.mountain=NULL}: Character scalar. Line color
- in mountain-type plots, defaults to the setting of \code{col}.}
-
- \item{}{\code{span=0.2}: Numeric scalar. Parameter controlling
+ \item{}{\code{degree=1}: Numeric scalar. Parameter controlling
the loess calculation for smooth and mountain-type plots.
See \code{\link{panel.loess}} for details.}
- \item{}{\code{transformation=NULL}: Function. Applied to the
- data matrix prior to plotting or when calling the \code{score}
- method. The function should accept exactly one input argument
- and its return value needs to be a numeric vector which can
- be coerced back into a data matrix of identical dimensionality
- as the input data.}
-
- \item{}{\code{box.ratio=1}: Numeric scalar. Parameter controlling
+ \item{}{\code{do.out=TRUE}: Logical scalar. Parameter controlling
the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
- \item{}{\code{varwidth=FALSE}: Logical scalar. Parameter
- controlling the boxplot appearance. See \code{\link{panel.bwplot}}
+ \item{}{\code{evaluation=50}: Numeric scalar. Parameter
+ controlling the loess calculation for smooth and mountain-type
+ plots. See \code{\link{panel.loess}} for details.}
+
+ \item{}{\code{factor=0.5}: Numeric scalar. Factor to control
+ amount of jittering in xy-type plots. See \code{\link{panel.xyplot}}
for details.}
\item{}{\code{family="symmetric"}: Character scalar. Parameter
controlling the loess calculation for smooth and mountain-type
plots. See \code{\link{panel.loess}} for details.}
- \item{}{\code{separator=0}: Numeric scalar. Number of pixels
- used to separate individual samples in heatmap-type plots.}
+ \item{}{\code{fill.confint=NULL}: Character vector. Fill colors
+ for the confidence intervals for confint-type plots.}
- \item{}{\code{ncolor=100}: Integer scalar. The number of colors
- for the 'gradient' plotting type}
+ \item{}{\code{fill.histogram=NULL}: Character scalar. Fill
+ color in histogram-type plots, defaults to the setting of
+ \code{fill}.}
- \item{}{\code{stats=X[[44]]}: Function. Parameter controlling
- the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
+ \item{}{\code{fill.horizon=c("#B41414", "#E03231", "#F7A99C",
+ "#9FC8DC", "#468CC8", "#0165B3")}: The fill colors for the
+ segments in the \code{horizon}-type plot. This should be a
+ vector of length six, where the first three entries are the
+ colors for positive changes, and the latter three entries
+ are the colors for negative changes. Defaults to a red-blue
+ color scheme. See \code{\link{horizonplot}} for details.}
- \item{}{\code{amount=NULL}: Numeric scalar. Amount of jittering
- in xy-type plots. See \code{\link{panel.xyplot}} for details.}
+ \item{}{\code{fill.mountain=c("#CCFFFF", "#FFCCFF")}: Character
+ vector of length 2. Fill color in mountain-type and polygon-type
+ plots.}
- \item{}{\code{na.rm=FALSE}: Boolean controlling whether to
- discard all NA values when plotting or to keep empty spaces for NAs}
+ \item{}{\code{fontface.legend=NULL}: Integer or character
+ scalar. The font face for the legend text.}
- \item{}{\code{lwd.baseline=NULL}: Numeric scalar. Line width
- of the optional baseline, defaults to the setting of \code{lwd}.}
+ \item{}{\code{fontfamily.legend=NULL}: Integer or character
+ scalar. The font family for the legend text.}
- \item{}{\code{windowSize=NULL}: Numeric scalar. The size of
- the running window when the value of \code{window} is negative.}
+ \item{}{\code{fontsize.legend=NULL}: Numeric scalar. The pixel
+ size for the legend text.}
- \item{}{\code{lty.mountain=NULL}: Character or numeric scalar.
- Line type in mountain-type plots, defaults to the setting of
- \code{lty}.}
+ \item{}{\code{fontcolor.legend="#808080"}: Integer or character
+ scalar. The font color for the legend text.}
+
+ \item{}{\code{gradient=c("#F7FBFF", "#DEEBF7", "#C6DBEF",
+ "#9ECAE1", "#6BAED6", "#4292C6", "#2171B5", "#08519C",
+ "#08306B")}: Character vector. The base colors for the
+ \code{gradient} plotting type or the \code{heatmap} type with
+ a single group. When plotting heatmaps with more than one
+ group, the \code{col} parameter can be used to control the
+ group color scheme, however the gradient will always be from
+ white to 'col' and thus does not offer as much flexibility
+ as this \code{gradient} parameter.}
+
+ \item{}{\code{groups=NULL}: Vector coercable to a factor.
+ Optional sample grouping. See 'Details' section in
+ \code{\linkS4class{DataTrack}} for further information.}
+
+ \item{}{\code{horizon.origin=0}: The baseline relative to which
+ changes are indicated on the \code{horizon}-type plot. See
+ \code{\link{horizonplot}} for details.}
+
+ \item{}{\code{horizon.scale=NULL}: The scale for each of the
+ segments in the \code{horizon}-type plot. Defaults to 1/3 of
+ the absolute data range. See \code{\link{horizonplot}} for details.}
\item{}{\code{jitter.x=FALSE}: Logical scalar. Toggle on
jittering on the x axis in xy-type plots. See \code{\link{panel.xyplot}}
@@ -430,48 +503,94 @@ getScheme(name=getOption("Gviz.scheme"))
jittering on the y axis in xy-type plots. See \code{\link{panel.xyplot}}
for details.}
- \item{}{\code{groups=NULL}: Vector coercable to a factor.
- Optional sample grouping. See 'Details' section in
- \code{\linkS4class{DataTrack}} for further information.}
+ \item{}{\code{levels.fos=NULL}: Numeric scalar. Parameter
+ controlling the boxplot appearance. See \code{\link{panel.bwplot}}
+ for details.}
+
+ \item{}{\code{legend=TRUE}: Boolean triggering the addition of
+ a legend to the track to indicate groups. This only has an
+ effect if at least two groups are present.}
+
+ \item{}{\code{lineheight.legend=NULL}: Numeric scalar. The line
+ height for the legend text.}
\item{}{\code{lty.baseline=NULL}: Character or numeric scalar.
Line type of the optional baseline, defaults to the setting
of \code{lty}.}
- \item{}{\code{col.baseline=NULL}: Character scalar. Color for
- the optional baseline, defaults to the setting of \code{col}.}
+ \item{}{\code{lty.mountain=NULL}: Character or numeric scalar.
+ Line type in mountain-type and polygon-type plots, defaults
+ to the setting of \code{lty}.}
- \item{}{\code{evaluation=50}: Numeric scalar. Parameter
- controlling the loess calculation for smooth and mountain-type
- plots. See \code{\link{panel.loess}} for details.}
+ \item{}{\code{lwd.baseline=NULL}: Numeric scalar. Line width
+ of the optional baseline, defaults to the setting of \code{lwd}.}
- \item{}{\code{fill.mountain=c("#CCFFFF", "#FFCCFF")}: Character
- vector of length 2. Fill color in mountain-type plots.}
+ \item{}{\code{lwd.mountain=NULL}: Numeric scalar. Line width
+ in mountain-type and polygon-type plots, defaults to the
+ setting of \code{lwd}.}
- \item{}{\code{factor=0.5}: Numeric scalar. Factor to control
- amount of jittering in xy-type plots. See \code{\link{panel.xyplot}}
+ \item{}{\code{min.distance=0}: Numeric scalar. The mimimum
+ distance in pixel below which to collapse ranges.}
+
+ \item{}{\code{na.rm=FALSE}: Boolean controlling whether to
+ discard all NA values when plotting or to keep empty spaces for NAs}
+
+ \item{}{\code{ncolor=100}: Integer scalar. The number of colors
+ for the 'gradient' plotting type}
+
+ \item{}{\code{notch.frac=0.5}: Numeric scalar. Parameter
+ controlling the boxplot appearance. See \code{\link{panel.bwplot}}
for details.}
- \item{}{\code{do.out=TRUE}: Logical scalar. Parameter controlling
+ \item{}{\code{notch=FALSE}: Logical scalar. Parameter controlling
the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
- \item{}{\code{col.histogram="#808080"}: Character scalar. Line
- color in histogram-type plots.}
+ \item{}{\code{pch=20}: Integer scalar. The type of glyph used
+ for plotting symbols.}
- \item{}{\code{aggregation="mean"}: Function or character scalar.
- Used to aggregate values in windows or for collapsing
- overlapping items. The function has to accept a numeric vector
- as a single input parameter and has to return a numeric scalar
- with the aggregated value. Alternatively, one of the predefined
- options \code{mean}, \code{median} \code{sum}, \code{min},
- \code{max} or \code{extreme} can be supplied as a character
- scalar. Defaults to \code{mean}.}
+ \item{}{\code{separator=0}: Numeric scalar. Number of pixels
+ used to separate individual samples in heatmap- and horizon-type
+ plots.}
- \item{}{\code{coef=1.5}: Numeric scalar. Parameter controlling
+ \item{}{\code{showColorBar=TRUE}: Boolean. Indicate the data
+ range color mapping in the axis for 'heatmap' or 'gradient' types.}
+
+ \item{}{\code{showSampleNames=FALSE}: Boolean. Display the
+ names of the individual samples in a heatmap or a horizon plot.}
+
+ \item{}{\code{size=NULL}: Numeric scalar. The relative size of
+ the track. Can be overridden in the \code{\link{plotTracks}}
+ function. By default the size will be set automatically based
+ on the selected plotting type.}
+
+ \item{}{\code{span=0.2}: Numeric scalar. Parameter controlling
+ the loess calculation for smooth and mountain-type plots.
+ See \code{\link{panel.loess}} for details.}
+
+ \item{}{\code{stackedBars=TRUE}: Logical scalar. When there
+ are several data groups, draw the histogram-type plots as
+ stacked barplots or grouped side by side.}
+
+ \item{}{\code{stats=X[[i]]}: Function. Parameter controlling
the boxplot appearance. See \code{\link{panel.bwplot}} for details.}
- \item{}{\code{lwd.mountain=NULL}: Numeric scalar. Line width
- in mountain-type plots, defaults to the setting of \code{lwd}.}
+ \item{}{\code{transformation=NULL}: Function. Applied to the
+ data matrix prior to plotting or when calling the \code{score}
+ method. The function should accept exactly one input argument
+ and its return value needs to be a numeric vector which can
+ be coerced back into a data matrix of identical dimensionality
+ as the input data.}
+
+ \item{}{\code{type="p"}: Character vector. The plot type, one
+ or several in \code{c("p","l", "b", "a", "a_confint", "s",
+ "g", "r", "S", "confint", "smooth", "histogram", "mountain",
+ "polygon", "h", "boxplot", "gradient", "heatmap", "horizon")}.
+ See 'Details' section in \code{\linkS4class{DataTrack}} for
+ more information on the individual plotting types.}
+
+ \item{}{\code{varwidth=FALSE}: Logical scalar. Parameter
+ controlling the boxplot appearance. See \code{\link{panel.bwplot}}
+ for details.}
\item{}{\code{window=NULL}: Numeric or character scalar.
Aggregate the rows values of the data matrix to \code{window}
@@ -480,7 +599,14 @@ getScheme(name=getOption("Gviz.scheme"))
window of size \code{windowSize} using the same aggregation
method. Alternatively, the special value \code{auto} causes
the function to determine the optimal window size to avoid
- overplotting.}
+ overplotting, and \code{fixed} uses fixed-size windows of
+ size \code{windowSize}.}
+
+ \item{}{\code{windowSize=NULL}: Numeric scalar. The size of
+ the running window when the value of \code{window} is negative.}
+
+ \item{}{\code{ylim=NULL}: Numeric vector of length 2. The range
+ of the y-axis scale.}
}
@@ -488,130 +614,150 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text.}
+ \item{}{\code{alpha=1}: Numeric scalar. The transparency for
+ all track items.}
- \item{}{\code{fontsize=12}: Numeric scalar. The font size for
- all text.}
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
- \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
- number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{background.panel="transparent"}: Integer or
+ character scalar. The background color of the content panel.}
- \item{}{\code{fontcolor="black"}: Integer or character scalar.
- The font color for all text.}
+ \item{}{\code{background.title="lightgray"}: Integer or character
+ scalar. The background color for the title panel.}
- \item{}{\code{lwd=1}: Numeric scalar. Default line width setting
- for all plotting elements, unless there is a more specific
- control defined elsewhere.}
+ \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
+ factor for the axis annotation. Defaults to \code{NULL}, in
+ which case it is automatically determined based on the
+ available space.}
+
+ \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
+ factor for the title panel. This effects the fontsize of both
+ the title and the axis, if any. Defaults to \code{NULL},
+ which means that the text size is automatically adjusted to
+ the available space.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
The font and line color for the y axis, if any.}
- \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
-
- \item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
-
- \item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panels.}
-
- \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ \item{}{\code{col.border.title="white"}: Integer or character
+ scalar. The border color for the title panels.}
- \item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ \item{}{\code{col.frame="lightgray"}: Integer or character
+ scalar. The line color used for the panel frame, if
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
- plot a title panel. Although this can be set individually
- for each track, in multi-track plots as created by
- \code{\link{plotTracks}} there will still be an empty
- placeholder in case any of the other tracks include a title.
- The same holds true for axes. Note that the the title panel
- background color could be set to transparent in order to
- completely hide it.}
-
- \item{}{\code{lty="solid"}: Numeric scalar. Default line type
- setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
-
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
\code{col} parameter.}
- \item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
-
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global \code{col} parameter.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
+ \item{}{\code{col.title="white"}: Integer or character scalar.
+ The border color for the title panels}
- \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
- number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{fill="lightgray"}: Integer or character scalar.
+ Default fill color setting for all plotting elements, unless
+ there is a more specific control defined elsewhere.}
- \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
- factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ \item{}{\code{fontcolor="black"}: Integer or character scalar.
+ The font color for all text, unless a more specific definition
+ exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
The font face for the title panels.}
+ \item{}{\code{fontface=1}: Integer or character scalar. The
+ font face for all text, unless a more specific definition exists.}
+
+ \item{}{\code{fontfamily.title="sans"}: Integer or character
+ scalar. The font family for the title panels.}
+
+ \item{}{\code{fontfamily="sans"}: Integer or character scalar.
+ The font family for all text, unless a more specific definition
+ exists.}
+
+ \item{}{\code{fontsize=12}: Numeric scalar. The font size for
+ all text, unless a more specific definition exists.}
+
+ \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
+ track when plotting.}
+
+ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
+ number of horizontal grid lines, see \code{\link{panel.grid}}
+ for details.}
+
\item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text.}
+ height for all text, unless a more specific definition exists.}
- \item{}{\code{fill="lightgray"}: Integer or character scalar.
- Default fill color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ \item{}{\code{lty.grid="solid"}: Integer or character scalar.
+ Default line type for grid lines, both when \code{type=="g"}
+ in \code{\link{DataTrack}}s and when display parameter
+ \code{grid==TRUE}.}
+
+ \item{}{\code{lty="solid"}: Numeric scalar. Default line type
+ setting for all plotting elements, unless there is a more
+ specific control defined elsewhere.}
+
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
+
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
\item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
and when display parameter \code{grid==TRUE}.}
- \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
- factor for the title panel. This effects the fontsize of both
- the title and the axis, if any. Defaults to \code{NULL},
- which means that the text size is automatically adjusted to
- the available space.}
-
- \item{}{\code{col.frame="lightgray"}: Integer or character
- scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \item{}{\code{lwd=1}: Numeric scalar. Default line width setting
+ for all plotting elements, unless there is a more specific
+ control defined elsewhere.}
\item{}{\code{min.height=3}: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See \code{\link{collapsing}}
for details.}
- \item{}{\code{col="#0080FF"}: Integer or character scalar.
- Default line color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
- \item{}{\code{lty.grid="solid"}: Integer or character scalar.
- Default line type for grid lines, both when \code{type=="g"}
- in \code{\link{DataTrack}}s and when display parameter
- \code{grid==TRUE}.}
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{rotation.title=90}: The rotation angle for the
+ text in the title panel. Even though this can be adjusted,
+ the automatic resizing of the title panel will currently not
+ work, so use at own risk.}
+
+ \item{}{\code{rotation=0}: The rotation angle for all text
+ unless a more specific definiton exists.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).}
- \item{}{\code{fontfamily="sans"}: Integer or character scalar.
- The font family for all text.}
+ \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
+ plot a title panel. Although this can be set individually
+ for each track, in multi-track plots as created by
+ \code{\link{plotTracks}} there will still be an empty
+ placeholder in case any of the other tracks include a title.
+ The same holds true for axes. Note that the the title panel
+ background color could be set to transparent in order to
+ completely hide it.}
+
+ \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
+ number of vertical grid lines, see \code{\link{panel.grid}}
+ for details.}
}
@@ -621,39 +767,67 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{fontsize=10}: Numeric scalar. The font size for
- the chromosome name text.}
-
\item{}{\code{background.title="transparent"}: Character scalar.
The background color for the title panel. Defaults to omit
the background.}
- \item{}{\code{fontcolor="#808080"}: Character scalar. The font
- color for the chromosome name text.}
-
- \item{}{\code{size=NULL}: Numeric scalar. The relative size of
- the track. Defaults to automatic size setting. Can be overridden
- in the \code{\link{plotTracks}} function.}
+ \item{}{\code{bevel=0.45}: Numeric scalar, between 0 and 1.
+ The level of smoothness for the two ends of the ideogram.}
- \item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title
- panel. Defaults to omit the title panel.}
+ \item{}{\code{cex.bands=0.7}: Numeric scalar. The font expansion
+ factor for the chromosome band identifier text.}
\item{}{\code{cex=0.8}: Numeric scalar. The overall font
expansion factor for the chromosome name text.}
+ \item{}{\code{col="red"}: Character scalar. The border color
+ used for the highlighting of the currently displayed genomic
+ region.}
+
+ \item{}{\code{col.border.title="transparent"}: Integer or
+ character scalar. The border color for the title panels.}
+
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
+
\item{}{\code{fill="#FFE3E6"}: Character scalar. The fill color
used for the highlighting of the currently displayed genomic
region.}
+ \item{}{\code{fontface=1}: Character scalar. The font face for
+ the chromosome name text.}
+
+ \item{}{\code{fontfamily="sans"}: Character scalar. The font
+ family for the chromosome name text.}
+
+ \item{}{\code{fontcolor="#808080"}: Character scalar. The font
+ color for the chromosome name text.}
+
+ \item{}{\code{fontsize=10}: Numeric scalar. The font size for
+ the chromosome name text.}
+
+ \item{}{\code{outline=FALSE}: Logical scalar. Add borders to
+ the individual chromosome staining bands.}
+
+ \item{}{\code{showBandId=FALSE}: Logical scalar. Show the
+ identifier for the chromosome bands if there is space for it.}
+
+ \item{}{\code{lty=1}: Character or integer scalar. The line
+ type used for the highlighting of the currently displayed
+ genomic region.}
+
+ \item{}{\code{lwd=1}: Numeric scalar. The line width used for
+ the highlighting of the currently displayed genomic region.}
+
\item{}{\code{showId=TRUE}: Logical scalar. Indicate the
chromosome name next to the ideogram.}
- \item{}{\code{col="red"}: Character scalar. The border color
- used for the highlighting of the currently displayed genomic
- region.}
+ \item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title
+ panel. Defaults to omit the title panel.}
- \item{}{\code{bevel=0.45}: Numeric scalar, between 0 and 1.
- The level of smoothness for the two ends of the ideogram.}
+ \item{}{\code{size=NULL}: Numeric scalar. The relative size of
+ the track. Defaults to automatic size setting. Can also be
+ overridden in the \code{\link{plotTracks}} function.}
}
@@ -661,113 +835,118 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text.}
-
- \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
- number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{alpha=1}: Numeric scalar. The transparency for
+ all track items.}
- \item{}{\code{lwd=1}: Numeric scalar. Default line width setting
- for all plotting elements, unless there is a more specific
- control defined elsewhere.}
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
- \item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ \item{}{\code{background.panel="transparent"}: Integer or
+ character scalar. The background color of the content panel.}
- \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
+ factor for the axis annotation. Defaults to \code{NULL}, in
+ which case it is automatically determined based on the
+ available space.}
- \item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
+ factor for the title panel. This effects the fontsize of both
+ the title and the axis, if any. Defaults to \code{NULL},
+ which means that the text size is automatically adjusted to
+ the available space.}
- \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ \item{}{\code{col.axis="white"}: Integer or character scalar.
+ The font and line color for the y axis, if any.}
- \item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ \item{}{\code{col.frame="lightgray"}: Integer or character
+ scalar. The line color used for the panel frame, if
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{lty="solid"}: Numeric scalar. Default line type
- setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
-
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
\code{col} parameter.}
- \item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
-
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global \code{col} parameter.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
-
- \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
- number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{col.title="white"}: Integer or character scalar.
+ The border color for the title panels}
- \item{}{\code{collapse=TRUE}: Boolean controlling wether to
+ \item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
details.}
- \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
- factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
-
\item{}{\code{fontface.title=2}: Integer or character scalar.
The font face for the title panels.}
- \item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text.}
-
- \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
- for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ \item{}{\code{fontfamily.title="sans"}: Integer or character
+ scalar. The font family for the title panels.}
- \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
- factor for the title panel. This effects the fontsize of both
- the title and the axis, if any. Defaults to \code{NULL},
- which means that the text size is automatically adjusted to
- the available space.}
+ \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
+ track when plotting.}
- \item{}{\code{col.frame="lightgray"}: Integer or character
- scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
+ of a grid.}
- \item{}{\code{min.height=3}: Numeric scalar. The minimum range
- height in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
+ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
+ number of horizontal grid lines, see \code{\link{panel.grid}}
for details.}
+ \item{}{\code{lineheight=1}: Numeric scalar. The font line
+ height for all text, unless a more specific definition exists.}
+
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
+
+ \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
+ for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
\code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \item{}{\code{min.height=3}: Numeric scalar. The minimum range
+ height in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
+
+ \item{}{\code{rotation.title=90}: The rotation angle for the
+ text in the title panel. Even though this can be adjusted,
+ the automatic resizing of the title panel will currently not
+ work, so use at own risk.}
+
+ \item{}{\code{rotation=0}: The rotation angle for all text
+ unless a more specific definiton exists.}
+
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).}
- \item{}{\code{fontfamily="sans"}: Integer or character scalar.
- The font family for all text.}
+ \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
+ number of vertical grid lines, see \code{\link{panel.grid}}
+ for details.}
}
@@ -777,73 +956,137 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
+ \item{}{\code{arrowHeadWidth=30}: Numeric scalar. The width of
+ the arrow head in pixels if \code{shape} is \code{fixedArrow}.}
+
+ \item{}{\code{arrowHeadMaxWidth=40}: Numeric scalar. The maximum
+ width of the arrow head in pixels if \code{shape} is \code{arrow}.}
+
+ \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion
+ factor for the group-level annotation.}
+
+ \item{}{\code{cex=1}: Numeric scalar. The font expansion factor
+ for item identifiers.}
+
+ \item{}{\code{col.line="darkgray"}: Character scalar. The color
+ used for connecting lines between grouped items. Defaults to
+ a light gray, but if set to \code{NULL} the same color as
+ for the first item in the group is used.}
+
+ \item{}{\code{col="transparent"}: Character or integer scalar.
+ The border color for all track items.}
+
+ \item{}{\code{featureAnnotation=NULL}: Character scalar. Add
+ annotation information to the individual track elements. This
+ can be a value in \code{id}, \code{group} or \code{feature}.
+ Defaults to \code{id}. Only works if \code{showFeatureId} is
+ not \code{FALSE}.}
+
+ \item{}{\code{fill="lightblue"}: Character or integer scalar.
+ The fill color for untyped items. This is also used to connect
+ grouped items. See \code{\link{grouping}} for details.}
+
+ \item{}{\code{fontfamily.group="sans"}: Character scalar. The
+ font family for the group-level annotation.}
+
+ \item{}{\code{fontcolor.group="#808080"}: Character or integer
+ scalar. The font color for the group-level annotation.}
+
+ \item{}{\code{fontcolor.item="white"}: Character or integer
+ scalar. The font color for item identifiers.}
+
\item{}{\code{fontface.group=2}: Numeric scalar. The font face
for the group-level annotation.}
- \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control
- whether to plot the individual track item identifiers.}
+ \item{}{\code{fontsize.group=12}: Numeric scalar. The font size
+ for the group-level annotation.}
- \item{}{\code{fontsize=12}: Numeric scalar. The font size for
- item identifiers.}
+ \item{}{\code{groupAnnotation=NULL}: Character scalar. Add
+ annotation information as group labels. This can be a value
+ in \code{id}, \code{group} or \code{feature}. Defaults to
+ \code{group}. Only works if \code{showId} is not \code{FALSE}.}
- \item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a
- color gradient to show the amount of overplotting for collapsed
- items. This implies that \code{collapse==TRUE}}
+ \item{}{\code{just.group="left"}: Character scalar. the
+ justification of group labels. Either \code{left}, \code{right},
+ \code{above} or \code{below}.}
\item{}{\code{lex=1}: Numeric scalar. The line expansion factor
for all track items. This is also used to connect grouped
items. See \code{\link{grouping}} for details.}
- \item{}{\code{fontcolor="white"}: Character or integer scalar.
- The font color for item identifiers.}
+ \item{}{\code{lineheight=1}: Numeric scalar. The font line
+ height for item identifiers.}
- \item{}{\code{fontfamily="sans"}: Character scalar. The font
- family for item identifiers.}
+ \item{}{\code{lty="solid"}: Character or integer scalar. The
+ line type for all track items. This is also used to connect
+ grouped items. See \code{\link{grouping}} for details.}
+
+ \item{}{\code{lwd=1}: Integer scalar. The line width for all
+ track items. This is also used to connect grouped items. See
+ \code{\link{grouping}} for details.}
+
+ \item{}{\code{mergeGroups=FALSE}: Logical scalar. Merge fully
+ overlapping groups if \code{collapse==TRUE}.}
+
+ \item{}{\code{min.height=3}: Numeric scalar. The minimum range
+ height in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details. For feathered bars indicating the strandedness
+ of grouped items this also controls the height of the arrow
+ feathers.}
+
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
- \item{}{\code{size=1}: Numeric scalar. The relative size of
- the track. Can be overridden in the \code{\link{plotTracks}}
- function.}
+ \item{}{\code{rotation=0}: Numeric scalar. The degree of text
+ rotation for item identifiers.}
- \item{}{\code{lwd=1}: Integer scalar. The line width for all
- track items. This is also used to connect grouped items. See
- \code{\link{grouping}} for details.}
+ \item{}{\code{rotation.group=0}: Numeric scalar. The degree of
+ text rotation for group labels.}
- \item{}{\code{lty="solid"}: Character or integer scalar. The
- line type for all track items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ \item{}{\code{rotation.item=0}: Numeric scalar. The degree of
+ text rotation for item identifiers.}
\item{}{\code{shape="arrow"}: Character scalar. The shape in
which to display the track items. Currently only \code{box},
- \code{arrow}, \code{ellipse}, and \code{smallArrow} are
- implemented.}
-
- \item{}{\code{cex=1}: Numeric scalar. The font expansion factor
- for item identifiers.}
+ \code{arrow}, \code{fixedArrow}, \code{ellipse}, and
+ \code{smallArrow} are implemented.}
- \item{}{\code{fontface=1}: Integer scalar. The font face for
- item identifiers.}
-
- \item{}{\code{fill="lightblue"}: Character or integer scalar.
- The fill color for untyped items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control
+ whether to plot the individual track item identifiers.}
\item{}{\code{showId=FALSE}: Logical scalar. Control whether
to annotate individual groups.}
- \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion
- factor for the group-level annotation.}
+ \item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a
+ color gradient to show the amount of overplotting for collapsed
+ items. This implies that \code{collapse==TRUE}}
- \item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for item identifiers.}
+ \item{}{\code{size=1}: Numeric scalar. The relative size of
+ the track. Can be overridden in the \code{\link{plotTracks}}
+ function.}
- \item{}{\code{fontcolor.group="#808080"}: Character or integer
- scalar. The font color for the group-level annotation.}
+ }
- \item{}{\code{col="transparent"}: Character or integer scalar.
- The border color for all track items.}
+ \bold{\emph{Inherited from class StackedTrack:}}
- \item{}{\code{rotation=0}: Numeric scalar. The degree of text
- rotation for item identifiers.}
+ \describe{
+
+ \item{}{\code{stackHeight=0.75}: Numeric between 0 and 1.
+ Controls the vertical size and spacing between stacked
+ elements. The number defines the proportion of the total
+ available space for the stack that is used to draw the glyphs.
+ E.g., a value of 0.5 means that half of the available vertical
+ drawing space (for each stacking line) is used for the glyphs,
+ and thus one quarter of the available space each is used for
+ spacing above and below the glyph. Defaults to 0.75.}
+
+ \item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse
+ the y-ordering of stacked items. I.e., features that are
+ plotted on the bottom-most stacks will be moved to the top-most
+ stack and vice versa.}
}
@@ -851,91 +1094,84 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
- number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
-
- \item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ \item{}{\code{alpha=1}: Numeric scalar. The transparency for
+ all track items.}
- \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
- \item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ \item{}{\code{background.panel="transparent"}: Integer or
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panels.}
+ scalar. The background color for the title panel.}
- \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
+ factor for the axis annotation. Defaults to \code{NULL}, in
+ which case it is automatically determined based on the
+ available space.}
- \item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
+ factor for the title panel. This effects the fontsize of both
+ the title and the axis, if any. Defaults to \code{NULL},
+ which means that the text size is automatically adjusted to
+ the available space.}
+
+ \item{}{\code{col.axis="white"}: Integer or character scalar.
+ The font and line color for the y axis, if any.}
+
+ \item{}{\code{col.border.title="white"}: Integer or character
+ scalar. The border color for the title panels.}
+
+ \item{}{\code{col.frame="lightgray"}: Integer or character
+ scalar. The line color used for the panel frame, if
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
- plot a title panel. Although this can be set individually
- for each track, in multi-track plots as created by
- \code{\link{plotTracks}} there will still be an empty
- placeholder in case any of the other tracks include a title.
- The same holds true for axes. Note that the the title panel
- background color could be set to transparent in order to
- completely hide it.}
-
- \item{}{\code{col.line=NULL}: Integer or character scalar.
- Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
-
- \item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
-
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global \code{col} parameter.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
-
- \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
- number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{col.title="white"}: Integer or character scalar.
+ The border color for the title panels}
- \item{}{\code{collapse=TRUE}: Boolean controlling wether to
+ \item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
details.}
- \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
- factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ \item{}{\code{fontcolor="black"}: Integer or character scalar.
+ The font color for all text, unless a more specific definition
+ exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
The font face for the title panels.}
- \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
- for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ \item{}{\code{fontface=1}: Integer or character scalar. The
+ font face for all text, unless a more specific definition exists.}
- \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
- factor for the title panel. This effects the fontsize of both
- the title and the axis, if any. Defaults to \code{NULL},
- which means that the text size is automatically adjusted to
- the available space.}
+ \item{}{\code{fontfamily.title="sans"}: Integer or character
+ scalar. The font family for the title panels.}
- \item{}{\code{col.frame="lightgray"}: Integer or character
- scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \item{}{\code{fontfamily="sans"}: Integer or character scalar.
+ The font family for all text, unless a more specific definition
+ exists.}
- \item{}{\code{min.height=3}: Numeric scalar. The minimum range
- height in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
+ \item{}{\code{fontsize=12}: Numeric scalar. The font size for
+ all text, unless a more specific definition exists.}
+
+ \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
+ track when plotting.}
+
+ \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
+ of a grid.}
+
+ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
+ number of horizontal grid lines, see \code{\link{panel.grid}}
for details.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
@@ -943,17 +1179,46 @@ getScheme(name=getOption("Gviz.scheme"))
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
+
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
+
+ \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
+ for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
+ and when display parameter \code{grid==TRUE}.}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
\code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
+
+ \item{}{\code{rotation.title=90}: The rotation angle for the
+ text in the title panel. Even though this can be adjusted,
+ the automatic resizing of the title panel will currently not
+ work, so use at own risk.}
+
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).}
+ \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
+ plot a title panel. Although this can be set individually
+ for each track, in multi-track plots as created by
+ \code{\link{plotTracks}} there will still be an empty
+ placeholder in case any of the other tracks include a title.
+ The same holds true for axes. Note that the the title panel
+ background color could be set to transparent in order to
+ completely hide it.}
+
+ \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
+ number of vertical grid lines, see \code{\link{panel.grid}}
+ for details.}
+
}
}
@@ -962,20 +1227,65 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{showExonId=FALSE}: Logical scalar. Control whether
- to plot the individual exon identifiers.}
+ \item{}{\code{arrowHeadWidth=10}: Numeric scalar. The width of
+ the arrow head in pixels if \code{shape} is \code{fixedArrow}.}
+
+ \item{}{\code{arrowHeadMaxWidth=20}: Numeric scalar. The maximum
+ width of the arrow head in pixels if \code{shape} is \code{arrow}.}
+
+ \item{}{\code{col=NULL}: Character or integer scalar. The border
+ color for all track items. Defaults to using the same color
+ as in \code{fill}, also taking into account different track
+ \code{features}.}
+
+ \item{}{\code{collapseTranscripts=FALSE}: Logical or character
+ scalar. Can be one in \code{gene}, \code{longest}, \code{shortest}
+ or \code{meta}. Merge all transcripts of the same gene into
+ one single gene model. In the case of \code{gene} (or
+ \code{TRUE}), this will only keep the start location of the
+ first exon and the end location of the last exon from all
+ transcripts of the gene. For \code{shortest} and \code{longest},
+ only the longest or shortest transcript model is retained.
+ For \code{meta}, a meta-transcript containing the union of
+ all exons is formed (essentially identical to the operation
+ \code{reduce(geneModel)}).}
+
+ \item{}{\code{exonAnnotation=NULL}: Character scalar. Add
+ annotation information to the individual exon models. This
+ can be a value in \code{symbol}, \code{gene}, \code{transcript},
+ \code{exon} or \code{feature}. Defaults to \code{exon}. Only
+ works if \code{showExonId} is not \code{FALSE}.}
+
+ \item{}{\code{fill="orange"}: Character or integer scalar. The
+ fill color for untyped items. This is also used to connect
+ grouped items. See \code{\link{grouping}} for details.}
+
+ \item{}{\code{min.distance=0}: Numeric scalar. The minimum
+ pixel distance before collapsing range items, only if
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for
+ details. Note that a value larger than 0 may lead to UTR
+ regions being merged to CDS regions, which in most cases is
+ not particularly useful.}
\item{}{\code{shape=c("smallArrow", "box")}: Character scalar.
The shape in which to display the track items. Currently only
\code{box}, \code{arrow}, \code{ellipse}, and \code{smallArrow}
are implemented.}
- \item{}{\code{geneSymbols=TRUE}: Logical scalar. Use human-readable
- gene symbols or gene IDs for the transcript annotation.}
+ \item{}{\code{showExonId=NULL}: Logical scalar. Control whether
+ to plot the individual exon identifiers.}
- \item{}{\code{fill="orange"}: Character or integer scalar. The
- fill color for untyped items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ \item{}{\code{thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5",
+ "3UTR", "5UTR", "miRNA", "lincRNA", "three_prime_UTR",
+ "five_prime_UTR")}: Character vector. A listing of feature
+ types that should be drawn with thin boxes. Typically those
+ are non-coding elements.}
+
+ \item{}{\code{transcriptAnnotation=NULL}: Character scalar.
+ Add annotation information as transcript labels. This can be
+ a value in \code{symbol}, \code{gene}, \code{transcript},
+ \code{exon} or \code{feature}. Defaults to \code{symbol}.
+ Only works if \code{showId} is not \code{FALSE}.}
}
@@ -983,64 +1293,119 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
+ \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion
+ factor for the group-level annotation.}
+
+ \item{}{\code{cex=1}: Numeric scalar. The font expansion factor
+ for item identifiers.}
+
+ \item{}{\code{col.line="darkgray"}: Character scalar. The color
+ used for connecting lines between grouped items. Defaults to
+ a light gray, but if set to \code{NULL} the same color as
+ for the first item in the group is used.}
+
+ \item{}{\code{featureAnnotation=NULL}: Character scalar. Add
+ annotation information to the individual track elements. This
+ can be a value in \code{id}, \code{group} or \code{feature}.
+ Defaults to \code{id}. Only works if \code{showFeatureId} is
+ not \code{FALSE}.}
+
+ \item{}{\code{fontfamily.group="sans"}: Character scalar. The
+ font family for the group-level annotation.}
+
+ \item{}{\code{fontcolor.group="#808080"}: Character or integer
+ scalar. The font color for the group-level annotation.}
+
+ \item{}{\code{fontcolor.item="white"}: Character or integer
+ scalar. The font color for item identifiers.}
+
\item{}{\code{fontface.group=2}: Numeric scalar. The font face
for the group-level annotation.}
- \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control
- whether to plot the individual track item identifiers.}
+ \item{}{\code{fontsize.group=12}: Numeric scalar. The font size
+ for the group-level annotation.}
- \item{}{\code{fontsize=12}: Numeric scalar. The font size for
- item identifiers.}
+ \item{}{\code{groupAnnotation=NULL}: Character scalar. Add
+ annotation information as group labels. This can be a value
+ in \code{id}, \code{group} or \code{feature}. Defaults to
+ \code{group}. Only works if \code{showId} is not \code{FALSE}.}
- \item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a
- color gradient to show the amount of overplotting for collapsed
- items. This implies that \code{collapse==TRUE}}
+ \item{}{\code{just.group="left"}: Character scalar. the
+ justification of group labels. Either \code{left}, \code{right},
+ \code{above} or \code{below}.}
\item{}{\code{lex=1}: Numeric scalar. The line expansion factor
for all track items. This is also used to connect grouped
items. See \code{\link{grouping}} for details.}
- \item{}{\code{fontcolor="white"}: Character or integer scalar.
- The font color for item identifiers.}
-
- \item{}{\code{fontfamily="sans"}: Character scalar. The font
- family for item identifiers.}
+ \item{}{\code{lineheight=1}: Numeric scalar. The font line
+ height for item identifiers.}
- \item{}{\code{size=1}: Numeric scalar. The relative size of
- the track. Can be overridden in the \code{\link{plotTracks}}
- function.}
+ \item{}{\code{lty="solid"}: Character or integer scalar. The
+ line type for all track items. This is also used to connect
+ grouped items. See \code{\link{grouping}} for details.}
\item{}{\code{lwd=1}: Integer scalar. The line width for all
track items. This is also used to connect grouped items. See
\code{\link{grouping}} for details.}
- \item{}{\code{lty="solid"}: Character or integer scalar. The
- line type for all track items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ \item{}{\code{mergeGroups=FALSE}: Logical scalar. Merge fully
+ overlapping groups if \code{collapse==TRUE}.}
- \item{}{\code{cex=1}: Numeric scalar. The font expansion factor
- for item identifiers.}
+ \item{}{\code{min.height=3}: Numeric scalar. The minimum range
+ height in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details. For feathered bars indicating the strandedness
+ of grouped items this also controls the height of the arrow
+ feathers.}
+
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{rotation=0}: Numeric scalar. The degree of text
+ rotation for item identifiers.}
- \item{}{\code{fontface=1}: Integer scalar. The font face for
- item identifiers.}
+ \item{}{\code{rotation.group=0}: Numeric scalar. The degree of
+ text rotation for group labels.}
+
+ \item{}{\code{rotation.item=0}: Numeric scalar. The degree of
+ text rotation for item identifiers.}
+
+ \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control
+ whether to plot the individual track item identifiers.}
\item{}{\code{showId=FALSE}: Logical scalar. Control whether
to annotate individual groups.}
- \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion
- factor for the group-level annotation.}
+ \item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a
+ color gradient to show the amount of overplotting for collapsed
+ items. This implies that \code{collapse==TRUE}}
- \item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for item identifiers.}
+ \item{}{\code{size=1}: Numeric scalar. The relative size of
+ the track. Can be overridden in the \code{\link{plotTracks}}
+ function.}
- \item{}{\code{fontcolor.group="#808080"}: Character or integer
- scalar. The font color for the group-level annotation.}
+ }
- \item{}{\code{col="transparent"}: Character or integer scalar.
- The border color for all track items.}
+ \bold{\emph{Inherited from class StackedTrack:}}
- \item{}{\code{rotation=0}: Numeric scalar. The degree of text
- rotation for item identifiers.}
+ \describe{
+
+ \item{}{\code{stackHeight=0.75}: Numeric between 0 and 1.
+ Controls the vertical size and spacing between stacked
+ elements. The number defines the proportion of the total
+ available space for the stack that is used to draw the glyphs.
+ E.g., a value of 0.5 means that half of the available vertical
+ drawing space (for each stacking line) is used for the glyphs,
+ and thus one quarter of the available space each is used for
+ spacing above and below the glyph. Defaults to 0.75.}
+
+ \item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse
+ the y-ordering of stacked items. I.e., features that are
+ plotted on the bottom-most stacks will be moved to the top-most
+ stack and vice versa.}
}
@@ -1048,91 +1413,84 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
- number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
-
- \item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ \item{}{\code{alpha=1}: Numeric scalar. The transparency for
+ all track items.}
- \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
- \item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ \item{}{\code{background.panel="transparent"}: Integer or
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panels.}
+ scalar. The background color for the title panel.}
+
+ \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
+ factor for the axis annotation. Defaults to \code{NULL}, in
+ which case it is automatically determined based on the
+ available space.}
+
+ \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
+ factor for the title panel. This effects the fontsize of both
+ the title and the axis, if any. Defaults to \code{NULL},
+ which means that the text size is automatically adjusted to
+ the available space.}
+
+ \item{}{\code{col.axis="white"}: Integer or character scalar.
+ The font and line color for the y axis, if any.}
- \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ \item{}{\code{col.border.title="white"}: Integer or character
+ scalar. The border color for the title panels.}
- \item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ \item{}{\code{col.frame="lightgray"}: Integer or character
+ scalar. The line color used for the panel frame, if
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
- plot a title panel. Although this can be set individually
- for each track, in multi-track plots as created by
- \code{\link{plotTracks}} there will still be an empty
- placeholder in case any of the other tracks include a title.
- The same holds true for axes. Note that the the title panel
- background color could be set to transparent in order to
- completely hide it.}
-
- \item{}{\code{col.line=NULL}: Integer or character scalar.
- Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
-
- \item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
-
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global \code{col} parameter.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
-
- \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
- number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{col.title="white"}: Integer or character scalar.
+ The border color for the title panels}
- \item{}{\code{collapse=TRUE}: Boolean controlling wether to
+ \item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
details.}
- \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
- factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ \item{}{\code{fontcolor="black"}: Integer or character scalar.
+ The font color for all text, unless a more specific definition
+ exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
The font face for the title panels.}
- \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
- for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ \item{}{\code{fontface=1}: Integer or character scalar. The
+ font face for all text, unless a more specific definition exists.}
- \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
- factor for the title panel. This effects the fontsize of both
- the title and the axis, if any. Defaults to \code{NULL},
- which means that the text size is automatically adjusted to
- the available space.}
+ \item{}{\code{fontfamily.title="sans"}: Integer or character
+ scalar. The font family for the title panels.}
- \item{}{\code{col.frame="lightgray"}: Integer or character
- scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \item{}{\code{fontfamily="sans"}: Integer or character scalar.
+ The font family for all text, unless a more specific definition
+ exists.}
- \item{}{\code{min.height=3}: Numeric scalar. The minimum range
- height in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
+ \item{}{\code{fontsize=12}: Numeric scalar. The font size for
+ all text, unless a more specific definition exists.}
+
+ \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
+ track when plotting.}
+
+ \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
+ of a grid.}
+
+ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
+ number of horizontal grid lines, see \code{\link{panel.grid}}
for details.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
@@ -1140,17 +1498,42 @@ getScheme(name=getOption("Gviz.scheme"))
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
- \item{}{\code{min.distance=1}: Numeric scalar. The minimum
- pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
+
+ \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
+ for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
+ and when display parameter \code{grid==TRUE}.}
+
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
+
+ \item{}{\code{rotation.title=90}: The rotation angle for the
+ text in the title panel. Even though this can be adjusted,
+ the automatic resizing of the title panel will currently not
+ work, so use at own risk.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).}
+ \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
+ plot a title panel. Although this can be set individually
+ for each track, in multi-track plots as created by
+ \code{\link{plotTracks}} there will still be an empty
+ placeholder in case any of the other tracks include a title.
+ The same holds true for axes. Note that the the title panel
+ background color could be set to transparent in order to
+ completely hide it.}
+
+ \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
+ number of vertical grid lines, see \code{\link{panel.grid}}
+ for details.}
+
}
}
@@ -1159,40 +1542,44 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{scRNA_pseudogene="darkorange2"}: Character or
- integer scalar. Fill color for annotation objects of type
- 'scRNA_pseudogene'.}
-
- \item{}{\code{miRNA_pseudogene="cornsilk"}: Character or integer
- scalar. Fill color for annotation objects of type
- 'miRNA_pseudogene'.}
+ \item{}{\code{C_segment="burlywood4"}: Character or integer
+ scalar. Fill color for annotation objects of type 'C_segment'.}
\item{}{\code{D_segment="lightblue"}: Character or integer
scalar. Fill color for annotation objects of type 'C_segment'.}
- \item{}{\code{scRNA="darkorange"}: Character or integer scalar.
- Fill color for annotation objects of type 'scRNA'.}
-
\item{}{\code{J_segment="dodgerblue2"}: Character or integer
scalar. Fill color for annotation objects of type 'C_segment'.}
+ \item{}{\code{Mt_rRNA="yellow"}: Character or integer scalar.
+ Fill color for annotation objects of type 'Mt_rRNA'.}
+
+ \item{}{\code{Mt_tRNA="darkgoldenrod"}: Character or integer
+ scalar. Fill color for annotation objects of type 'Mt_tRNA'.}
+
\item{}{\code{Mt_tRNA_pseudogene="darkgoldenrod1"}: Character
or integer scalar. Fill color for annotation objects of type
'Mt_tRNA_pseudogene'.}
- \item{}{\code{Mt_rRNA="yellow"}: Character or integer scalar.
- Fill color for annotation objects of type 'Mt_rRNA'.}
+ \item{}{\code{V_segment="aquamarine"}: Character or integer
+ scalar. Fill color for annotation objects of type 'V_segment'.}
- \item{}{\code{tRNA_pseudogene="antiquewhite3"}: Character or
- integer scalar. Fill color for annotation objects of type
- 'tRNA_pseudogene'.}
+ \item{}{\code{miRNA="cornflowerblue"}: Character or integer
+ scalar. Fill color for annotation objects of type 'L_segment'.}
- \item{}{\code{rRNA_pseudogene="darkolivegreen"}: Character or
+ \item{}{\code{miRNA_pseudogene="cornsilk"}: Character or integer
+ scalar. Fill color for annotation objects of type
+ 'miRNA_pseudogene'.}
+
+ \item{}{\code{misc_RNA="cornsilk3"}: Character or integer
+ scalar. Fill color for annotation objects of type 'misc_RNA'.}
+
+ \item{}{\code{misc_RNA_pseudogene="cornsilk4"}: Character or
integer scalar. Fill color for annotation objects of type
- 'rRNA_pseudogene'.}
+ 'misc_RNA_pseudogene'.}
- \item{}{\code{miRNA="cornflowerblue"}: Character or integer
- scalar. Fill color for annotation objects of type 'L_segment'.}
+ \item{}{\code{protein_coding="#FFD58A"}: Character or integer
+ scalar. Fill color for annotation objects of type 'protein_coding'.}
\item{}{\code{pseudogene="brown1"}: Character or integer scalar.
Fill color for annotation objects of type 'pseudogene'.}
@@ -1200,42 +1587,47 @@ getScheme(name=getOption("Gviz.scheme"))
\item{}{\code{rRNA="darkolivegreen1"}: Character or integer
scalar. Fill color for annotation objects of type 'rRNA'.}
- \item{}{\code{protein_coding="gold4"}: Character or integer
- scalar. Fill color for annotation objects of type 'protein_coding'.}
-
- \item{}{\code{Mt_tRNA="darkgoldenrod"}: Character or integer
- scalar. Fill color for annotation objects of type 'Mt_tRNA'.}
+ \item{}{\code{rRNA_pseudogene="darkolivegreen"}: Character or
+ integer scalar. Fill color for annotation objects of type
+ 'rRNA_pseudogene'.}
\item{}{\code{retrotransposed="blueviolet"}: Character or
integer scalar. Fill color for annotation objects of type
'retrotransposed'.}
+ \item{}{\code{scRNA="gold4"}: Character or integer scalar. Fill
+ color for annotation objects of type 'scRNA'.}
+
+ \item{}{\code{scRNA_pseudogene="darkorange2"}: Character or
+ integer scalar. Fill color for annotation objects of type
+ 'scRNA_pseudogene'.}
+
\item{}{\code{snRNA="coral"}: Character or integer scalar. Fill
color for annotation objects of type 'snRNA'.}
- \item{}{\code{V_segment="aquamarine"}: Character or integer
- scalar. Fill color for annotation objects of type 'V_segment'.}
-
\item{}{\code{snRNA_pseudogene="coral3"}: Character or integer
scalar. Fill color for annotation objects of type
'snRNA_pseudogene'.}
- \item{}{\code{misc_RNA="cornsilk3"}: Character or integer
- scalar. Fill color for annotation objects of type 'misc_RNA'.}
-
- \item{}{\code{misc_RNA_pseudogene="cornsilk4"}: Character or
- integer scalar. Fill color for annotation objects of type
- 'misc_RNA_pseudogene'.}
+ \item{}{\code{snoRNA="cyan"}: Character or integer scalar. Fill
+ color for annotation objects of type 'snoRNA'.}
\item{}{\code{snoRNA_pseudogene="cyan2"}: Character or integer
scalar. Fill color for annotation objects of type
'snoRNA_pseudogene'.}
- \item{}{\code{snoRNA="cyan"}: Character or integer scalar. Fill
- color for annotation objects of type 'snoRNA'.}
+ \item{}{\code{tRNA_pseudogene="antiquewhite3"}: Character or
+ integer scalar. Fill color for annotation objects of type
+ 'tRNA_pseudogene'.}
- \item{}{\code{C_segment="burlywood4"}: Character or integer
- scalar. Fill color for annotation objects of type 'C_segment'.}
+ \item{}{\code{utr3="#FFD58A"}: FIXME: PLEASE ADD PARAMETER
+ DESCRIPTION.}
+
+ \item{}{\code{utr5="#FFD58A"}: FIXME: PLEASE ADD PARAMETER
+ DESCRIPTION.}
+
+ \item{}{\code{verbose=FALSE}: Logical scalar. Report data
+ loading events from Bioamart or retrieval from cache.}
}
@@ -1243,20 +1635,65 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{showExonId=FALSE}: Logical scalar. Control whether
- to plot the individual exon identifiers.}
+ \item{}{\code{arrowHeadWidth=10}: Numeric scalar. The width of
+ the arrow head in pixels if \code{shape} is \code{fixedArrow}.}
+
+ \item{}{\code{arrowHeadMaxWidth=20}: Numeric scalar. The maximum
+ width of the arrow head in pixels if \code{shape} is \code{arrow}.}
+
+ \item{}{\code{col=NULL}: Character or integer scalar. The border
+ color for all track items. Defaults to using the same color
+ as in \code{fill}, also taking into account different track
+ \code{features}.}
+
+ \item{}{\code{collapseTranscripts=FALSE}: Logical or character
+ scalar. Can be one in \code{gene}, \code{longest}, \code{shortest}
+ or \code{meta}. Merge all transcripts of the same gene into
+ one single gene model. In the case of \code{gene} (or
+ \code{TRUE}), this will only keep the start location of the
+ first exon and the end location of the last exon from all
+ transcripts of the gene. For \code{shortest} and \code{longest},
+ only the longest or shortest transcript model is retained.
+ For \code{meta}, a meta-transcript containing the union of
+ all exons is formed (essentially identical to the operation
+ \code{reduce(geneModel)}).}
+
+ \item{}{\code{exonAnnotation=NULL}: Character scalar. Add
+ annotation information to the individual exon models. This
+ can be a value in \code{symbol}, \code{gene}, \code{transcript},
+ \code{exon} or \code{feature}. Defaults to \code{exon}. Only
+ works if \code{showExonId} is not \code{FALSE}.}
+
+ \item{}{\code{fill="orange"}: Character or integer scalar. The
+ fill color for untyped items. This is also used to connect
+ grouped items. See \code{\link{grouping}} for details.}
+
+ \item{}{\code{min.distance=0}: Numeric scalar. The minimum
+ pixel distance before collapsing range items, only if
+ \code{collapse==TRUE}. See \code{\link{collapsing}} for
+ details. Note that a value larger than 0 may lead to UTR
+ regions being merged to CDS regions, which in most cases is
+ not particularly useful.}
\item{}{\code{shape=c("smallArrow", "box")}: Character scalar.
The shape in which to display the track items. Currently only
\code{box}, \code{arrow}, \code{ellipse}, and \code{smallArrow}
are implemented.}
- \item{}{\code{geneSymbols=TRUE}: Logical scalar. Use human-readable
- gene symbols or gene IDs for the transcript annotation.}
+ \item{}{\code{showExonId=NULL}: Logical scalar. Control whether
+ to plot the individual exon identifiers.}
- \item{}{\code{fill="orange"}: Character or integer scalar. The
- fill color for untyped items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ \item{}{\code{thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5",
+ "3UTR", "5UTR", "miRNA", "lincRNA", "three_prime_UTR",
+ "five_prime_UTR")}: Character vector. A listing of feature
+ types that should be drawn with thin boxes. Typically those
+ are non-coding elements.}
+
+ \item{}{\code{transcriptAnnotation=NULL}: Character scalar.
+ Add annotation information as transcript labels. This can be
+ a value in \code{symbol}, \code{gene}, \code{transcript},
+ \code{exon} or \code{feature}. Defaults to \code{symbol}.
+ Only works if \code{showId} is not \code{FALSE}.}
}
@@ -1264,64 +1701,119 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
+ \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion
+ factor for the group-level annotation.}
+
+ \item{}{\code{cex=1}: Numeric scalar. The font expansion factor
+ for item identifiers.}
+
+ \item{}{\code{col.line="darkgray"}: Character scalar. The color
+ used for connecting lines between grouped items. Defaults to
+ a light gray, but if set to \code{NULL} the same color as
+ for the first item in the group is used.}
+
+ \item{}{\code{featureAnnotation=NULL}: Character scalar. Add
+ annotation information to the individual track elements. This
+ can be a value in \code{id}, \code{group} or \code{feature}.
+ Defaults to \code{id}. Only works if \code{showFeatureId} is
+ not \code{FALSE}.}
+
+ \item{}{\code{fontfamily.group="sans"}: Character scalar. The
+ font family for the group-level annotation.}
+
+ \item{}{\code{fontcolor.group="#808080"}: Character or integer
+ scalar. The font color for the group-level annotation.}
+
+ \item{}{\code{fontcolor.item="white"}: Character or integer
+ scalar. The font color for item identifiers.}
+
\item{}{\code{fontface.group=2}: Numeric scalar. The font face
for the group-level annotation.}
- \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control
- whether to plot the individual track item identifiers.}
+ \item{}{\code{fontsize.group=12}: Numeric scalar. The font size
+ for the group-level annotation.}
- \item{}{\code{fontsize=12}: Numeric scalar. The font size for
- item identifiers.}
+ \item{}{\code{groupAnnotation=NULL}: Character scalar. Add
+ annotation information as group labels. This can be a value
+ in \code{id}, \code{group} or \code{feature}. Defaults to
+ \code{group}. Only works if \code{showId} is not \code{FALSE}.}
- \item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a
- color gradient to show the amount of overplotting for collapsed
- items. This implies that \code{collapse==TRUE}}
+ \item{}{\code{just.group="left"}: Character scalar. the
+ justification of group labels. Either \code{left}, \code{right},
+ \code{above} or \code{below}.}
\item{}{\code{lex=1}: Numeric scalar. The line expansion factor
for all track items. This is also used to connect grouped
items. See \code{\link{grouping}} for details.}
- \item{}{\code{fontcolor="white"}: Character or integer scalar.
- The font color for item identifiers.}
-
- \item{}{\code{fontfamily="sans"}: Character scalar. The font
- family for item identifiers.}
+ \item{}{\code{lineheight=1}: Numeric scalar. The font line
+ height for item identifiers.}
- \item{}{\code{size=1}: Numeric scalar. The relative size of
- the track. Can be overridden in the \code{\link{plotTracks}}
- function.}
+ \item{}{\code{lty="solid"}: Character or integer scalar. The
+ line type for all track items. This is also used to connect
+ grouped items. See \code{\link{grouping}} for details.}
\item{}{\code{lwd=1}: Integer scalar. The line width for all
track items. This is also used to connect grouped items. See
\code{\link{grouping}} for details.}
- \item{}{\code{lty="solid"}: Character or integer scalar. The
- line type for all track items. This is also used to connect
- grouped items. See \code{\link{grouping}} for details.}
+ \item{}{\code{mergeGroups=FALSE}: Logical scalar. Merge fully
+ overlapping groups if \code{collapse==TRUE}.}
- \item{}{\code{cex=1}: Numeric scalar. The font expansion factor
- for item identifiers.}
+ \item{}{\code{min.height=3}: Numeric scalar. The minimum range
+ height in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details. For feathered bars indicating the strandedness
+ of grouped items this also controls the height of the arrow
+ feathers.}
+
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{rotation=0}: Numeric scalar. The degree of text
+ rotation for item identifiers.}
+
+ \item{}{\code{rotation.group=0}: Numeric scalar. The degree of
+ text rotation for group labels.}
- \item{}{\code{fontface=1}: Integer scalar. The font face for
- item identifiers.}
+ \item{}{\code{rotation.item=0}: Numeric scalar. The degree of
+ text rotation for item identifiers.}
+
+ \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control
+ whether to plot the individual track item identifiers.}
\item{}{\code{showId=FALSE}: Logical scalar. Control whether
to annotate individual groups.}
- \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion
- factor for the group-level annotation.}
+ \item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a
+ color gradient to show the amount of overplotting for collapsed
+ items. This implies that \code{collapse==TRUE}}
- \item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for item identifiers.}
+ \item{}{\code{size=1}: Numeric scalar. The relative size of
+ the track. Can be overridden in the \code{\link{plotTracks}}
+ function.}
- \item{}{\code{fontcolor.group="#808080"}: Character or integer
- scalar. The font color for the group-level annotation.}
+ }
- \item{}{\code{col="transparent"}: Character or integer scalar.
- The border color for all track items.}
+ \bold{\emph{Inherited from class StackedTrack:}}
- \item{}{\code{rotation=0}: Numeric scalar. The degree of text
- rotation for item identifiers.}
+ \describe{
+
+ \item{}{\code{stackHeight=0.75}: Numeric between 0 and 1.
+ Controls the vertical size and spacing between stacked
+ elements. The number defines the proportion of the total
+ available space for the stack that is used to draw the glyphs.
+ E.g., a value of 0.5 means that half of the available vertical
+ drawing space (for each stacking line) is used for the glyphs,
+ and thus one quarter of the available space each is used for
+ spacing above and below the glyph. Defaults to 0.75.}
+
+ \item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse
+ the y-ordering of stacked items. I.e., features that are
+ plotted on the bottom-most stacks will be moved to the top-most
+ stack and vice versa.}
}
@@ -1329,91 +1821,84 @@ getScheme(name=getOption("Gviz.scheme"))
\describe{
- \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
- number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{alpha=1}: Numeric scalar. The transparency for
+ all track items.}
+
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
+
+ \item{}{\code{background.panel="transparent"}: Integer or
+ character scalar. The background color of the content panel.}
+
+ \item{}{\code{background.title="lightgray"}: Integer or character
+ scalar. The background color for the title panel.}
+
+ \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
+ factor for the axis annotation. Defaults to \code{NULL}, in
+ which case it is automatically determined based on the
+ available space.}
+
+ \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
+ factor for the title panel. This effects the fontsize of both
+ the title and the axis, if any. Defaults to \code{NULL},
+ which means that the text size is automatically adjusted to
+ the available space.}
\item{}{\code{col.axis="white"}: Integer or character scalar.
The font and line color for the y axis, if any.}
- \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
-
- \item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
-
- \item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panels.}
+ \item{}{\code{col.border.title="white"}: Integer or character
+ scalar. The border color for the title panels.}
- \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
-
- \item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ \item{}{\code{col.frame="lightgray"}: Integer or character
+ scalar. The line color used for the panel frame, if
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
- plot a title panel. Although this can be set individually
- for each track, in multi-track plots as created by
- \code{\link{plotTracks}} there will still be an empty
- placeholder in case any of the other tracks include a title.
- The same holds true for axes. Note that the the title panel
- background color could be set to transparent in order to
- completely hide it.}
-
- \item{}{\code{col.line=NULL}: Integer or character scalar.
- Default colors for plot lines. Usually the same as the global
- \code{col} parameter.}
-
- \item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
-
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global \code{col} parameter.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
-
- \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
- number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{col.title="white"}: Integer or character scalar.
+ The border color for the title panels}
- \item{}{\code{collapse=TRUE}: Boolean controlling wether to
+ \item{}{\code{collapse=TRUE}: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See \code{\link{collapsing}} for
details.}
- \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
- factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ \item{}{\code{fontcolor="black"}: Integer or character scalar.
+ The font color for all text, unless a more specific definition
+ exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
The font face for the title panels.}
- \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
- for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ \item{}{\code{fontface=1}: Integer or character scalar. The
+ font face for all text, unless a more specific definition exists.}
- \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
- factor for the title panel. This effects the fontsize of both
- the title and the axis, if any. Defaults to \code{NULL},
- which means that the text size is automatically adjusted to
- the available space.}
+ \item{}{\code{fontfamily.title="sans"}: Integer or character
+ scalar. The font family for the title panels.}
- \item{}{\code{col.frame="lightgray"}: Integer or character
- scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \item{}{\code{fontfamily="sans"}: Integer or character scalar.
+ The font family for all text, unless a more specific definition
+ exists.}
- \item{}{\code{min.height=3}: Numeric scalar. The minimum range
- height in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
+ \item{}{\code{fontsize=12}: Numeric scalar. The font size for
+ all text, unless a more specific definition exists.}
+
+ \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
+ track when plotting.}
+
+ \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
+ of a grid.}
+
+ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
+ number of horizontal grid lines, see \code{\link{panel.grid}}
for details.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
@@ -1421,17 +1906,42 @@ getScheme(name=getOption("Gviz.scheme"))
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
- \item{}{\code{min.distance=1}: Numeric scalar. The minimum
- pixel distance before collapsing range items, only if
- \code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
+
+ \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
+ for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
+ and when display parameter \code{grid==TRUE}.}
+
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
+
+ \item{}{\code{rotation.title=90}: The rotation angle for the
+ text in the title panel. Even though this can be adjusted,
+ the automatic resizing of the title panel will currently not
+ work, so use at own risk.}
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).}
+ \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
+ plot a title panel. Although this can be set individually
+ for each track, in multi-track plots as created by
+ \code{\link{plotTracks}} there will still be an empty
+ placeholder in case any of the other tracks include a title.
+ The same holds true for axes. Note that the the title panel
+ background color could be set to transparent in order to
+ completely hide it.}
+
+ \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
+ number of vertical grid lines, see \code{\link{panel.grid}}
+ for details.}
+
}
}
@@ -1449,9 +1959,13 @@ getScheme(name=getOption("Gviz.scheme"))
\item{}{\code{type="histogram"}: the plot type, one or several
in \code{c("p","l", "b", "a", "s", "g", "r", "S", "smooth",
- "histogram", "mountain", "h", "boxplot", "gradient", "heatmap")}.
- See the 'Details' section in \code{\linkS4class{DataTrack}}
- for more information on the individual plotting types.}
+ "histogram", "mountain", "polygon", "h", "boxplot", "gradient",
+ "heatmap", "horizon")}. See the 'Details' section in
+ \code{\linkS4class{DataTrack}} for more information on the
+ individual plotting types.}
+
+ \item{}{\code{fill="#0080ff"}: the fill color for the coverage
+ indicator.}
\item{}{\code{size=NULL}: the relative size of the track.
Defaults to size selection based on the underlying data. Can
@@ -1460,142 +1974,187 @@ getScheme(name=getOption("Gviz.scheme"))
\item{}{\code{collapse=FALSE}: collapse overlapping ranges and
aggregate the underlying data.}
- \item{}{\code{fill="#0080ff"}: the fill color for the coverage
- indicator.}
-
}
- \bold{\emph{Inherited from class GdObject:}}
+ \bold{\emph{Inherited from class StackedTrack:}}
\describe{
- \item{}{\code{fontface=1}: Integer or character scalar. The
- font face for all text.}
+ \item{}{\code{stackHeight=0.75}: Numeric between 0 and 1.
+ Controls the vertical size and spacing between stacked
+ elements. The number defines the proportion of the total
+ available space for the stack that is used to draw the glyphs.
+ E.g., a value of 0.5 means that half of the available vertical
+ drawing space (for each stacking line) is used for the glyphs,
+ and thus one quarter of the available space each is used for
+ spacing above and below the glyph. Defaults to 0.75.}
- \item{}{\code{fontsize=12}: Numeric scalar. The font size for
- all text.}
+ \item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse
+ the y-ordering of stacked items. I.e., features that are
+ plotted on the bottom-most stacks will be moved to the top-most
+ stack and vice versa.}
- \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
- number of horizontal grid lines, see \code{\link{panel.grid}}
- for details.}
+ }
- \item{}{\code{fontcolor="black"}: Integer or character scalar.
- The font color for all text.}
+ \bold{\emph{Inherited from class GdObject:}}
- \item{}{\code{lwd=1}: Numeric scalar. Default line width setting
- for all plotting elements, unless there is a more specific
- control defined elsewhere.}
+ \describe{
- \item{}{\code{col.axis="white"}: Integer or character scalar.
- The font and line color for the y axis, if any.}
+ \item{}{\code{alpha=1}: Numeric scalar. The transparency for
+ all track items.}
- \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
- of a grid.}
+ \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency
+ for the title panel.}
- \item{}{\code{fontfamily.title="sans"}: Integer or character
- scalar. The font family for the title panels.}
+ \item{}{\code{background.panel="transparent"}: Integer or
+ character scalar. The background color of the content panel.}
\item{}{\code{background.title="lightgray"}: Integer or character
- scalar. The background color for the title panels.}
+ scalar. The background color for the title panel.}
- \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
- track when plotting.}
+ \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
+ factor for the axis annotation. Defaults to \code{NULL}, in
+ which case it is automatically determined based on the
+ available space.}
- \item{}{\code{alpha=1}: Numeric scalar. The transparency for
- all track items.}
+ \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
+ factor for the title panel. This effects the fontsize of both
+ the title and the axis, if any. Defaults to \code{NULL},
+ which means that the text size is automatically adjusted to
+ the available space.}
+
+ \item{}{\code{cex=1}: Numeric scalar. The overall font expansion
+ factor for all text and glyphs, unless a more specific
+ definition exists.}
+
+ \item{}{\code{col.axis="white"}: Integer or character scalar.
+ The font and line color for the y axis, if any.}
+
+ \item{}{\code{col.border.title="white"}: Integer or character
+ scalar. The border color for the title panels.}
+
+ \item{}{\code{col.frame="lightgray"}: Integer or character
+ scalar. The line color used for the panel frame, if
+ \code{frame==TRUE}}
\item{}{\code{col.grid="#808080"}: Integer or character scalar.
Default line color for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
- plot a title panel. Although this can be set individually
- for each track, in multi-track plots as created by
- \code{\link{plotTracks}} there will still be an empty
- placeholder in case any of the other tracks include a title.
- The same holds true for axes. Note that the the title panel
- background color could be set to transparent in order to
- completely hide it.}
-
- \item{}{\code{lty="solid"}: Numeric scalar. Default line type
- setting for all plotting elements, unless there is a more
- specific control defined elsewhere.}
-
\item{}{\code{col.line=NULL}: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
\code{col} parameter.}
- \item{}{\code{background.panel="transparent"}: Integer or
- character scalar. The background color of the content panel.}
-
\item{}{\code{col.symbol=NULL}: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global \code{col} parameter.}
- \item{}{\code{min.width=1}: Numeric scalar. The minimum range
- width in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
- for details.}
-
- \item{}{\code{cex=1}: Numeric scalar. The overall font expansion
- factor for all text.}
+ \item{}{\code{col.title="white"}: Integer or character scalar.
+ The border color for the title panels}
- \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
- number of vertical grid lines, see \code{\link{panel.grid}}
- for details.}
+ \item{}{\code{col="#0080FF"}: Integer or character scalar.
+ Default line color setting for all plotting elements, unless
+ there is a more specific control defined elsewhere.}
- \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion
- factor for the axis annotation. Defaults to \code{NULL}, in
- which case it is computed based on the available space.}
+ \item{}{\code{fontcolor="black"}: Integer or character scalar.
+ The font color for all text, unless a more specific definition
+ exists.}
\item{}{\code{fontface.title=2}: Integer or character scalar.
The font face for the title panels.}
- \item{}{\code{lineheight=1}: Numeric scalar. The font line
- height for all text.}
+ \item{}{\code{fontface=1}: Integer or character scalar. The
+ font face for all text, unless a more specific definition exists.}
- \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
- for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
- and when display parameter \code{grid==TRUE}.}
+ \item{}{\code{fontfamily.title="sans"}: Integer or character
+ scalar. The font family for the title panels.}
- \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion
- factor for the title panel. This effects the fontsize of both
- the title and the axis, if any. Defaults to \code{NULL},
- which means that the text size is automatically adjusted to
- the available space.}
+ \item{}{\code{fontfamily="sans"}: Integer or character scalar.
+ The font family for all text, unless a more specific definition
+ exists.}
- \item{}{\code{col.frame="lightgray"}: Integer or character
- scalar. The line color used for the panel frame, if
- \code{frame==TRUE}}
+ \item{}{\code{fontsize=12}: Numeric scalar. The font size for
+ all text, unless a more specific definition exists.}
- \item{}{\code{min.height=3}: Numeric scalar. The minimum range
- height in pixels to display. All ranges are expanded to this
- size in order to avoid rendering issues. See \code{\link{collapsing}}
+ \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the
+ track when plotting.}
+
+ \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting
+ of a grid.}
+
+ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the
+ number of horizontal grid lines, see \code{\link{panel.grid}}
for details.}
- \item{}{\code{col="#0080FF"}: Integer or character scalar.
- Default line color setting for all plotting elements, unless
- there is a more specific control defined elsewhere.}
+ \item{}{\code{lineheight=1}: Numeric scalar. The font line
+ height for all text, unless a more specific definition exists.}
\item{}{\code{lty.grid="solid"}: Integer or character scalar.
Default line type for grid lines, both when \code{type=="g"}
in \code{\link{DataTrack}}s and when display parameter
\code{grid==TRUE}.}
- \item{}{\code{col.title="white"}: Integer or character scalar.
- The font color for the title panels.}
+ \item{}{\code{lty="solid"}: Numeric scalar. Default line type
+ setting for all plotting elements, unless there is a more
+ specific control defined elsewhere.}
+
+ \item{}{\code{lwd.border.title=1}: Integer scalar. The border
+ width for the title panels.}
+
+ \item{}{\code{lwd.title=1}: Integer scalar. The border width
+ for the title panels}
+
+ \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width
+ for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s
+ and when display parameter \code{grid==TRUE}.}
+
+ \item{}{\code{lwd=1}: Numeric scalar. Default line width setting
+ for all plotting elements, unless there is a more specific
+ control defined elsewhere.}
\item{}{\code{min.distance=1}: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
\code{collapse==TRUE}. See \code{\link{collapsing}} for details.}
+ \item{}{\code{min.height=3}: Numeric scalar. The minimum range
+ height in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{min.width=1}: Numeric scalar. The minimum range
+ width in pixels to display. All ranges are expanded to this
+ size in order to avoid rendering issues. See \code{\link{collapsing}}
+ for details.}
+
+ \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the
+ plotting coordinates in 3' -> 5' direction if \code{TRUE}.
+ This will effectively mirror the plot on the vertical axis.}
+
+ \item{}{\code{rotation.title=90}: The rotation angle for the
+ text in the title panel. Even though this can be adjusted,
+ the automatic resizing of the title panel will currently not
+ work, so use at own risk.}
+
+ \item{}{\code{rotation=0}: The rotation angle for all text
+ unless a more specific definiton exists.}
+
\item{}{\code{showAxis=TRUE}: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).}
- \item{}{\code{fontfamily="sans"}: Integer or character scalar.
- The font family for all text.}
+ \item{}{\code{showTitle=TRUE}: Boolean controlling whether to
+ plot a title panel. Although this can be set individually
+ for each track, in multi-track plots as created by
+ \code{\link{plotTracks}} there will still be an empty
+ placeholder in case any of the other tracks include a title.
+ The same holds true for axes. Note that the the title panel
+ background color could be set to transparent in order to
+ completely hide it.}
+
+ \item{}{\code{v=-1}: Integer scalar. Parameter controlling the
+ number of vertical grid lines, see \code{\link{panel.grid}}
+ for details.}
}
@@ -1627,6 +2186,8 @@ getScheme(name=getOption("Gviz.scheme"))
\code{\link{grouping}}
+ \code{\link{horizonplot}}
+
\code{\link{panel.bwplot}}
\code{\link{panel.grid}}
@@ -1650,3 +2211,5 @@ getScheme(name=getOption("Gviz.scheme"))
+
+
diff --git a/vignettes/Gviz.Rnw b/vignettes/Gviz.Rnw
index f68a9a4..5e68eec 100644
--- a/vignettes/Gviz.Rnw
+++ b/vignettes/Gviz.Rnw
@@ -1743,7 +1743,7 @@ library(biomaRt)
bm <- useMart(host="may2012.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl")
fm <- Gviz:::.getBMFeatureMap()
-fm["symbol"] <- "external_gene_id"
+fm[["symbol"]] <- "external_gene_id"
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr7", start=20e6, end=21e6,name="ENSEMBL",
featureMap=fm, biomart=bm)
plotTracks(biomTrack, col.line=NULL, col=NULL, stackHeight=0.3)
@@ -2127,7 +2127,7 @@ and read pairs are connected by a bright gray line. Gaps in
the alignments are show by the connecting dark gray lines. Numbers of
reads supporting each gap can be visualized as ``sashimi plot''
\cite{Katz22012015} by adding \Rfunarg{``sashimi''} as an additional
-agument to the \Rfunarg{type} display parameter.
+agument to the \Rfunarg{type} display parameter.
The axis in the title panel shows the relationship between the line
width the the number of reads spanning a given junction. The height of
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