[med-svn] [r-bioc-cummerbund] 01/04: New upstream version 2.20.0
Andreas Tille
tille at debian.org
Thu Nov 9 10:14:38 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-cummerbund.
commit fe578f83d339bba06b60976e3847328ec9fe4805
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 9 11:07:24 2017 +0100
New upstream version 2.20.0
---
DESCRIPTION | 4 +-
NAMESPACE | 4 +-
R/database-setup.R | 15 +++++--
R/methods-CuffData.R | 3 +-
R/methods-CuffFeatureSet.R | 1 +
R/methods-CuffGene.R | 2 +-
README | 5 ++-
build/vignette.rds | Bin 302 -> 303 bytes
inst/doc/cummeRbund-example-workflow.pdf | Bin 170482 -> 170482 bytes
inst/doc/cummeRbund-manual.R | 72 +++++++++++++++----------------
inst/doc/cummeRbund-manual.Rnw | 2 +-
inst/doc/cummeRbund-manual.pdf | Bin 1370034 -> 1357444 bytes
vignettes/cummeRbund-manual.Rnw | 2 +-
13 files changed, 62 insertions(+), 48 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index eb1fda0..3954e31 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: cummeRbund
Title: Analysis, exploration, manipulation, and visualization of
Cufflinks high-throughput sequencing data.
-Version: 2.18.0
+Version: 2.20.0
Date: 2013-04-22
Author: L. Goff, C. Trapnell, D. Kelley
Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
@@ -22,4 +22,4 @@ biocViews: HighThroughputSequencing, HighThroughputSequencingData,
Infrastructure, DataImport, DataRepresentation, Visualization,
Bioinformatics, Clustering, MultipleComparisons, QualityControl
NeedsCompilation: no
-Packaged: 2017-04-24 23:11:44 UTC; biocbuild
+Packaged: 2017-10-30 23:19:40 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index e17ff94..2f00c80 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,8 +2,10 @@ import(methods)
#importFrom(graphics, plot)
importFrom(plyr, defaults)
+
importFrom(BiocGenerics, annotation)
-import(S4Vectors)
+#import(S4Vectors)
+
importFrom(Biobase, featureNames)
exportClasses(CuffSet,
diff --git a/R/database-setup.R b/R/database-setup.R
index 8bc7917..6c29e7d 100644
--- a/R/database-setup.R
+++ b/R/database-setup.R
@@ -204,6 +204,7 @@ loadGenes<-function(fpkmFile,
write("Writing geneData table",stderr())
#dbWriteTable(dbConn,'geneData',as.data.frame(genemelt[,c(1:2,5,3,4,6)]),row.names=F,append=T)
insert_SQL<-'INSERT INTO geneData VALUES(:tracking_id,:sample_name,:fpkm,:conf_hi,:conf_lo,:status)'
+ #write(insert_SQL,stderr())
bulk_insert(dbConn,insert_SQL,genemelt[,c(1:2,5,3,4,6)])
#######
@@ -224,12 +225,14 @@ loadGenes<-function(fpkmFile,
write("Writing geneExpDiffData table",stderr())
diffCols<-c(1,5:14)
-
+ colnames(diff)[colnames(diff)=="log2.fold_change."]<-"log2_fold_change" # Not sure why this is the only place this is screwy...
+
#debugging
#write(colnames(diff[,diffCols]),stderr())
#dbWriteTable(dbConn,'geneExpDiffData',diff[,diffCols],row.names=F,append=T)
- insert_SQL<-"INSERT INTO geneExpDiffData VALUES(:test_id,:sample_1,:sample_2,:status,:value_1,:value_2,?,:test_stat,:p_value,:q_value,:significant)"
+
+ insert_SQL<-"INSERT INTO geneExpDiffData VALUES(:test_id,:sample_1,:sample_2,:status,:value_1,:value_2,:log2_fold_change,:test_stat,:p_value,:q_value,:significant)"
bulk_insert(dbConn,insert_SQL,diff[,diffCols])
}else{
write(paste("No records found in", diffFile),stderr())
@@ -1759,7 +1762,8 @@ getSamplesFromColnames<-function(fpkmDF){
populateSampleTable<-function(samples,dbConn){
samples<-make.db.names(dbConn,samples,unique=FALSE)
- samples<-data.frame(index=c(1:length(samples)),sample_name=samples)
+ samples<-data.frame(sample_index=c(1:length(samples)),sample_name=samples)
+ #print(samples)
dbWriteTable(dbConn,'samples',samples,row.names=F,append=T)
}
@@ -1950,6 +1954,7 @@ readCufflinks<-function(dir = getwd(),
stop("Must provide a dbConn connection")
write("Reading GTF file",stderr())
+
gr<-import(gtfFile)
gr<-as(gr,"data.frame")
#gr$genome<-genomebuild
@@ -2014,7 +2019,9 @@ readCufflinks<-function(dir = getwd(),
tmpS <- split(tmp, values(tmp)$transcript_id)
if(verbose) message('Attempting to create the splicings data.frame')
splicings <- data.frame(
+
tx_id=rep(1:length(tmpS), elementNROWS(tmpS)),
+
exon_rank=as.integer(values(unlist(tmpS))$exon_number),
exon_chrom=as.character(seqnames(unlist(tmpS))),
exon_strand=as.character(strand(unlist(tmpS))),
@@ -2033,7 +2040,9 @@ readCufflinks<-function(dir = getwd(),
#create the db
if (verbose) message("Creating TranscriptDb")
+
tmpdb <- makeTxDb(transcripts, splicings, genes=genes)
+
if (verbose) message("Use saveFeatures() to save the database to a file")
return(tmpdb)
diff --git a/R/methods-CuffData.R b/R/methods-CuffData.R
index b048e57..880850f 100644
--- a/R/methods-CuffData.R
+++ b/R/methods-CuffData.R
@@ -777,6 +777,7 @@ setMethod("csVolcano",signature(object="CuffData"), .volcano)
p <-ggplot(dat) + geom_point(mapping,na.rm=TRUE,size=0.8) + scale_colour_manual(values = c("black","red")) + facet_grid(sample_1~sample_2)
p<- p + geom_vline(aes(xintercept=0),linetype=2)
+
p <- p + theme_bw() + xlab(bquote(paste(log[2],"(fold change)",sep=""))) + ylab(bquote(paste(-log[10],"(p value)",sep="")))
@@ -961,7 +962,7 @@ setMethod("MDSplot",signature(object="CuffData"),.MDSplot)
if(showPoints){
plot<- plot + geom_point(alpha=.4, size=0.8, aes(label=obsnames))
}
-
+
plot <- plot + geom_hline(aes(yintercept=0), size=.2) + geom_vline(aes(xintercept=0), size=.2) #+ geom_text(aes(label=shoutout),size=2,color="red")
datapc <- data.frame(varnames=rownames(PC$rotation), PC$rotation)
diff --git a/R/methods-CuffFeatureSet.R b/R/methods-CuffFeatureSet.R
index 47cce07..81b5350 100644
--- a/R/methods-CuffFeatureSet.R
+++ b/R/methods-CuffFeatureSet.R
@@ -1146,6 +1146,7 @@ setMethod("MDSplot",signature(object="CuffFeatureSet"),.MDSplot)
if(showPoints){
plot<- plot + geom_point(alpha=.4, size=0.8, aes(label=obsnames))
}
+
plot <- plot + geom_hline(aes(yintercept=0), size=.2) + geom_vline(aes(xintercept=0), size=.2) #+ geom_text(aes(label=shoutout),size=2,color="red")
datapc <- data.frame(varnames=rownames(PC$rotation), PC$rotation)
diff --git a/R/methods-CuffGene.R b/R/methods-CuffGene.R
index c23f368..45cc177 100644
--- a/R/methods-CuffGene.R
+++ b/R/methods-CuffGene.R
@@ -171,9 +171,9 @@ setMethod("genePlot",signature(object="CuffGene"),.plot)
#print(dat)
p<-ggplot(dat,aes(x="",y=fpkm,fill=tracking_id))
+
p<- p + geom_bar(stat="identity",position="fill",color="black")
-
p<- p + coord_polar(theta='y')
p<-p + scale_fill_hue(l=50,h.start=200) + scale_color_hue(l=50,h.start=200) + theme_bw()
diff --git a/README b/README
index a0a3f98..a70254b 100644
--- a/README
+++ b/README
@@ -10,9 +10,10 @@
Authors:
- Loyal A. Goff (1,2)
- Cole Trapnell (2)
-
+
Maintainer:
- - Loyal A. Goff <lgoff at csail.mit.edu>
+ - Loyal A. Goff <loyalgoff at jhmi.edu>
+
Creative Contributions & Support:
- John L. Rinn (2)
diff --git a/build/vignette.rds b/build/vignette.rds
index 5ed9f64..8d5e880 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/cummeRbund-example-workflow.pdf b/inst/doc/cummeRbund-example-workflow.pdf
index 8e5210f..a2aa155 100644
Binary files a/inst/doc/cummeRbund-example-workflow.pdf and b/inst/doc/cummeRbund-example-workflow.pdf differ
diff --git a/inst/doc/cummeRbund-manual.R b/inst/doc/cummeRbund-manual.R
index 792dcae..4b52535 100644
--- a/inst/doc/cummeRbund-manual.R
+++ b/inst/doc/cummeRbund-manual.R
@@ -548,42 +548,42 @@ plotTracks(genetrack)
###################################################
-### code chunk number 68: features_3
-###################################################
-trackList<-list()
-myStart<-min(features(myGene)$start)
-myEnd<-max(features(myGene)$end)
-myChr<-unique(features(myGene)$seqnames)
-genome<-'hg19'
-
-ideoTrack <- IdeogramTrack(genome = genome, chromosome = myChr)
-trackList<-c(trackList,ideoTrack)
-
-axtrack<-GenomeAxisTrack()
-trackList<-c(trackList,axtrack)
-
-genetrack<-makeGeneRegionTrack(myGene)
-genetrack
-
-trackList<-c(trackList,genetrack)
-
-biomTrack<-BiomartGeneRegionTrack(genome=genome,chromosome=as.character(myChr),
- start=myStart,end=myEnd,name="ENSEMBL",showId=T)
-
-trackList<-c(trackList,biomTrack)
-
-conservation <- UcscTrack(genome = genome, chromosome = myChr,
- track = "Conservation", table = "phyloP100wayAll",
- from = myStart-2000, to = myEnd+2000, trackType = "DataTrack",
- start = "start", end = "end", data = "score",
- type = "hist", window = "auto", col.histogram = "darkblue",
- fill.histogram = "darkblue", ylim = c(-3.7, 4),
- name = "Conservation")
-
-trackList<-c(trackList,conservation)
-
-plotTracks(trackList,from=myStart-2000,to=myEnd+2000)
-
+### code chunk number 68: features_3 (eval = FALSE)
+###################################################
+## trackList<-list()
+## myStart<-min(features(myGene)$start)
+## myEnd<-max(features(myGene)$end)
+## myChr<-unique(features(myGene)$seqnames)
+## genome<-'hg19'
+##
+## ideoTrack <- IdeogramTrack(genome = genome, chromosome = myChr)
+## trackList<-c(trackList,ideoTrack)
+##
+## axtrack<-GenomeAxisTrack()
+## trackList<-c(trackList,axtrack)
+##
+## genetrack<-makeGeneRegionTrack(myGene)
+## genetrack
+##
+## trackList<-c(trackList,genetrack)
+##
+## biomTrack<-BiomartGeneRegionTrack(genome=genome,chromosome=as.character(myChr),
+## start=myStart,end=myEnd,name="ENSEMBL",showId=T)
+##
+## trackList<-c(trackList,biomTrack)
+##
+## conservation <- UcscTrack(genome = genome, chromosome = myChr,
+## track = "Conservation", table = "phyloP100wayAll",
+## from = myStart-2000, to = myEnd+2000, trackType = "DataTrack",
+## start = "start", end = "end", data = "score",
+## type = "hist", window = "auto", col.histogram = "darkblue",
+## fill.histogram = "darkblue", ylim = c(-3.7, 4),
+## name = "Conservation")
+##
+## trackList<-c(trackList,conservation)
+##
+## plotTracks(trackList,from=myStart-2000,to=myEnd+2000)
+##
###################################################
diff --git a/inst/doc/cummeRbund-manual.Rnw b/inst/doc/cummeRbund-manual.Rnw
index 7ce98d0..c3a84ef 100644
--- a/inst/doc/cummeRbund-manual.Rnw
+++ b/inst/doc/cummeRbund-manual.Rnw
@@ -944,7 +944,7 @@ to add additional tracks from an external data source.
\textit{Note: This feature is now deprecated owing to developmental constraints.
It is still provided with cummeRbund, but is no longer supported.}
-<<features_3,fig=TRUE>>=
+<<features_3,fig=TRUE,eval=FALSE,echo=FALSE>>=
trackList<-list()
myStart<-min(features(myGene)$start)
myEnd<-max(features(myGene)$end)
diff --git a/inst/doc/cummeRbund-manual.pdf b/inst/doc/cummeRbund-manual.pdf
index cbde835..54b166b 100644
Binary files a/inst/doc/cummeRbund-manual.pdf and b/inst/doc/cummeRbund-manual.pdf differ
diff --git a/vignettes/cummeRbund-manual.Rnw b/vignettes/cummeRbund-manual.Rnw
index 7ce98d0..c3a84ef 100644
--- a/vignettes/cummeRbund-manual.Rnw
+++ b/vignettes/cummeRbund-manual.Rnw
@@ -944,7 +944,7 @@ to add additional tracks from an external data source.
\textit{Note: This feature is now deprecated owing to developmental constraints.
It is still provided with cummeRbund, but is no longer supported.}
-<<features_3,fig=TRUE>>=
+<<features_3,fig=TRUE,eval=FALSE,echo=FALSE>>=
trackList<-list()
myStart<-min(features(myGene)$start)
myEnd<-max(features(myGene)$end)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-cummerbund.git
More information about the debian-med-commit
mailing list