[med-svn] [r-bioc-limma] 01/04: Imported Upstream version 3.20.9+dfsg
Andreas Tille
tille at debian.org
Tue Sep 16 16:03:07 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-limma.
commit c310b4a96f437ece5329b3d2248bb1c77ba4a94c
Author: Andreas Tille <tille at debian.org>
Date: Tue Sep 16 17:33:29 2014 +0200
Imported Upstream version 3.20.9+dfsg
---
DESCRIPTION | 6 +++---
R/plotMDS.R | 14 +++++++-------
R/read-maimages.R | 4 ++--
R/venn.R | 14 +++++++-------
build/vignette.rds | Bin 230 -> 230 bytes
inst/doc/changelog.txt | 14 ++++++++++++++
inst/doc/intro.pdf | Bin 46191 -> 46191 bytes
inst/doc/usersguide.pdf | Bin 0 -> 1017047 bytes
man/plotMDS.Rd | 11 +++++------
vignettes/intro.Rnw | 49 ------------------------------------------------
10 files changed, 38 insertions(+), 74 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 557914d..67a4a30 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: limma
-Version: 3.20.7
-Date: 2014/06/24
+Version: 3.20.9
+Date: 2014/08/27
Title: Linear Models for Microarray Data
Description: Data analysis, linear models and differential expression for microarray data.
Author: Gordon Smyth [cre,aut], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Natalie Thorne [ctb], Davis McCarthy [ctb], Di Wu [ctb], Yifang Hu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]
@@ -19,4 +19,4 @@ biocViews: ExonArray, GeneExpression, Transcription,
ProprietaryPlatforms, TwoChannel, RNASeq, BatchEffect,
MultipleComparison, Normalization, Preprocessing,
QualityControl
-Packaged: 2014-06-26 02:22:20 UTC; biocbuild
+Packaged: 2014-08-28 02:01:52 UTC; biocbuild
diff --git a/R/plotMDS.R b/R/plotMDS.R
index 0999a01..9790bad 100644
--- a/R/plotMDS.R
+++ b/R/plotMDS.R
@@ -10,11 +10,11 @@ setMethod("show","MDS",function(object) {
plotMDS <- function(x,...) UseMethod("plotMDS")
-plotMDS.MDS <- function(x,labels=NULL,pch=NULL,col=NULL,cex=1,dim.plot=x$dim.plot,xlab=paste("Dimension",dim.plot[1]),ylab=paste("Dimension",dim.plot[2]),...)
+plotMDS.MDS <- function(x,labels=NULL,pch=NULL,cex=1,dim.plot=x$dim.plot,xlab=paste("Dimension",dim.plot[1]),ylab=paste("Dimension",dim.plot[2]),...)
# Method for MDS objects
# Create a new plot using MDS coordinates or distances previously created
# Gordon Smyth and Yifang Hu
-# 21 May 2011. Last modified 2 June 2014
+# 21 May 2011. Last modified 26 June 2014
{
# Check labels
if(is.null(labels) & is.null(pch)) {
@@ -33,7 +33,7 @@ plotMDS.MDS <- function(x,labels=NULL,pch=NULL,col=NULL,cex=1,dim.plot=x$dim.plo
# Make the plot
if(is.null(labels)){
# Plot symbols instead of text
- plot(x$x, x$y, pch = pch, xlab = xlab, ylab = ylab, col = col, cex = cex, ...)
+ plot(x$x, x$y, pch = pch, xlab = xlab, ylab = ylab, cex = cex, ...)
} else {
# Plot text. Need to estimate width of labels in plot coordinates.
# Estimate will be ok for default plot width, but maybe too small for smaller plots.
@@ -42,16 +42,16 @@ plotMDS.MDS <- function(x,labels=NULL,pch=NULL,col=NULL,cex=1,dim.plot=x$dim.plo
left.x <- x$x-StringRadius
right.x <- x$x+StringRadius
plot(c(left.x, right.x), c(x$y, x$y), type = "n", xlab = xlab, ylab = ylab, ...)
- text(x$x, x$y, labels = labels, col = col, cex = cex)
+ text(x$x, x$y, labels = labels, cex = cex, ...)
}
return(invisible(x))
}
-plotMDS.default <- function(x,top=500,labels=NULL,pch=NULL,col=NULL,cex=1,dim.plot=c(1,2),ndim=max(dim.plot),gene.selection="pairwise",xlab=paste("Dimension",dim.plot[1]),ylab=paste("Dimension",dim.plot[2]),...)
+plotMDS.default <- function(x,top=500,labels=NULL,pch=NULL,cex=1,dim.plot=c(1,2),ndim=max(dim.plot),gene.selection="pairwise",xlab=paste("Dimension",dim.plot[1]),ylab=paste("Dimension",dim.plot[2]),...)
# Multi-dimensional scaling with top-distance
# Di Wu and Gordon Smyth
-# 19 March 2009. Last modified 22 May 2014
+# 19 March 2009. Last modified 26 June 2014
{
# Check x
x <- as.matrix(x)
@@ -105,5 +105,5 @@ plotMDS.default <- function(x,top=500,labels=NULL,pch=NULL,col=NULL,cex=1,dim.pl
mds <- new("MDS",list(dim.plot=dim.plot,distance.matrix=dd,cmdscale.out=a1,top=top,gene.selection=gene.selection))
mds$x <- a1[,dim.plot[1]]
mds$y <- a1[,dim.plot[2]]
- plotMDS(mds,labels=labels,pch=pch,col=col,cex=cex,xlab=xlab,ylab=ylab,...)
+ plotMDS(mds,labels=labels,pch=pch,cex=cex,xlab=xlab,ylab=ylab,...)
}
diff --git a/R/read-maimages.R b/R/read-maimages.R
index 909621e..f5fd19e 100644
--- a/R/read-maimages.R
+++ b/R/read-maimages.R
@@ -4,7 +4,7 @@ read.maimages <- function(files=NULL,source="generic",path=NULL,ext=NULL,names=N
# Extracts an RG list from a set of two-color image analysis output files
# or an EListRaw from a set of one-color files
# Gordon Smyth.
-# 1 Nov 2002. Last revised 9 March 2012.
+# 1 Nov 2002. Last revised 27 August 2012.
{
# Begin checking input arguments
@@ -21,7 +21,7 @@ read.maimages <- function(files=NULL,source="generic",path=NULL,ext=NULL,names=N
source <- match.arg(source,c("generic","agilent","agilent.mean","agilent.median","arrayvision","arrayvision.ARM","arrayvision.MTM","bluefuse","genepix","genepix.mean","genepix.median","genepix.custom","imagene","imagene9","quantarray","scanarrayexpress","smd.old","smd","spot","spot.close.open"))
# source2 is the source type with qualifications removed
source2 <- strsplit(source,split=".",fixed=TRUE)[[1]][1]
- if(is.null(quote)) if(source=="agilent") quote <- "" else quote <- "\""
+ if(is.null(quote)) if(source2=="agilent") quote <- "" else quote <- "\""
if(source2=="imagene") return(read.imagene(files=files,path=path,ext=ext,names=names,columns=columns,other.columns=other.columns,wt.fun=wt.fun,verbose=verbose,sep=sep,quote=quote,...))
if(is.data.frame(files)) {
diff --git a/R/venn.R b/R/venn.R
index 18dd6a2..d8c42d9 100755
--- a/R/venn.R
+++ b/R/venn.R
@@ -161,9 +161,9 @@ vennDiagram <- function(object,include="both",names=NULL,mar=rep(1,4),cex=c(1.5,
rect(-20, -20, 420, 400)
elps <- cbind(162*cos(seq(0,2*pi,len=1000)), 108*sin(seq(0,2*pi,len=1000)))
polygon(relocate_elp(elps, 45, 130, 170),border=circle.col[1],lwd=lwd)
- polygon(relocate_elp(elps, 45, 200, 200),border=circle.col[1],lwd=lwd)
- polygon(relocate_elp(elps, 135, 200, 200),border=circle.col[1],lwd=lwd)
- polygon(relocate_elp(elps, 135, 270, 170),border=circle.col[1],lwd=lwd)
+ polygon(relocate_elp(elps, 45, 200, 200),border=circle.col[2],lwd=lwd)
+ polygon(relocate_elp(elps, 135, 200, 200),border=circle.col[3],lwd=lwd)
+ polygon(relocate_elp(elps, 135, 270, 170),border=circle.col[4],lwd=lwd)
text( 35, 315, names[1], cex=cex[1])
text(138, 350, names[2], cex=cex[1])
@@ -221,10 +221,10 @@ vennDiagram <- function(object,include="both",names=NULL,mar=rep(1,4),cex=c(1.5,
elps <- cbind(150*cos(seq(0,2*pi,len=1000)), 60*sin(seq(0,2*pi,len=1000)))
polygon(relocate_elp(elps, 90,200, 250),border=circle.col[1],lwd=lwd)
- polygon(relocate_elp(elps, 162,250, 220),border=circle.col[1],lwd=lwd)
- polygon(relocate_elp(elps, 234,250, 150),border=circle.col[1],lwd=lwd)
- polygon(relocate_elp(elps, 306,180, 125),border=circle.col[1],lwd=lwd)
- polygon(relocate_elp(elps, 378,145, 200),border=circle.col[1],lwd=lwd)
+ polygon(relocate_elp(elps, 162,250, 220),border=circle.col[2],lwd=lwd)
+ polygon(relocate_elp(elps, 234,250, 150),border=circle.col[3],lwd=lwd)
+ polygon(relocate_elp(elps, 306,180, 125),border=circle.col[4],lwd=lwd)
+ polygon(relocate_elp(elps, 378,145, 200),border=circle.col[5],lwd=lwd)
text( 50, 285, names[1],cex=cex[1])
text(200, 415, names[2],cex=cex[1])
diff --git a/build/vignette.rds b/build/vignette.rds
index 253b32f..ed236c7 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/changelog.txt b/inst/doc/changelog.txt
index f075d59..42fda6b 100755
--- a/inst/doc/changelog.txt
+++ b/inst/doc/changelog.txt
@@ -1,3 +1,17 @@
+27 August 2014: limma 3.20.8
+
+- Bug fix for read.maimages: default value for 'quote' was not being
+ set correctly for source="agilent.mean" or source="agilent.median".
+
+27 June 2014: limma 3.20.8
+
+- remove col argument from plotMDS(), as it handled by ... as are
+ other graphics arguments.
+
+- vennDiagram() now supports circles of different colors for any
+ number of circles. Previously this was supported only up to three
+ sets.
+
24 June 2014: limma 3.20.7
- update to helpMethods().
diff --git a/inst/doc/intro.pdf b/inst/doc/intro.pdf
index 78b9b67..10e4cb8 100644
Binary files a/inst/doc/intro.pdf and b/inst/doc/intro.pdf differ
diff --git a/inst/doc/usersguide.pdf b/inst/doc/usersguide.pdf
new file mode 100644
index 0000000..7508e02
Binary files /dev/null and b/inst/doc/usersguide.pdf differ
diff --git a/man/plotMDS.Rd b/man/plotMDS.Rd
index d6a7062..4db21df 100644
--- a/man/plotMDS.Rd
+++ b/man/plotMDS.Rd
@@ -12,11 +12,11 @@ Distances on the plot can be interpreted in terms of \emph{leading log2-fold-cha
}
\usage{
-\method{plotMDS}{default}(x, top=500, labels=NULL, pch=NULL, col=NULL, cex=1,
+\method{plotMDS}{default}(x, top=500, labels=NULL, pch=NULL, cex=1,
dim.plot=c(1,2), ndim=max(dim.plot), gene.selection="pairwise",
- xlab=paste("Dimension",dim.plot[1]), ylab=paste("Dimension",dim.plot[2]), ...)
-\method{plotMDS}{MDS}(x, labels=NULL, pch=NULL, col=NULL, cex=1, dim.plot=x$dim.plot,
- xlab=paste("Dimension",dim.plot[1]), ylab=paste("Dimension",dim.plot[2]),...)
+ xlab=paste("Dimension",dim.plot[1]), ylab=paste("Dimension",dim.plot[2]), \dots)
+\method{plotMDS}{MDS}(x, labels=NULL, pch=NULL, cex=1, dim.plot=x$dim.plot,
+ xlab=paste("Dimension",dim.plot[1]), ylab=paste("Dimension",dim.plot[2]), \dots)
}
\arguments{
@@ -24,14 +24,13 @@ Distances on the plot can be interpreted in terms of \emph{leading log2-fold-cha
\item{top}{number of top genes used to calculate pairwise distances.}
\item{labels}{character vector of sample names or labels. If \code{x} has no column names, then defaults the index of the samples.}
\item{pch}{plotting symbol or symbols. See \code{\link{points}} for possible values. Ignored if \code{labels} is non-\code{NULL}.}
- \item{col}{numeric or character vector of colors for the plotting characters.}
\item{cex}{numeric vector of plot symbol expansions.}
\item{dim.plot}{which two dimensions should be plotted, numeric vector of length two.}
\item{ndim}{number of dimensions in which data is to be represented}
\item{gene.selection}{character, \code{"pairwise"} to choose the top genes separately for each pairwise comparison between the samples or \code{"common"} to select the same genes for all comparisons}
\item{xlab}{title for the x-axis}
\item{ylab}{title for the y-axis}
- \item{...}{any other arguments are passed to \code{plot}.}
+ \item{\dots}{any other arguments are passed to \code{plot}, and also to \code{text} (if \code{pch} is \code{NULL}).}
}
\details{
diff --git a/vignettes/intro.Rnw b/vignettes/intro.Rnw
deleted file mode 100644
index 88f952a..0000000
--- a/vignettes/intro.Rnw
+++ /dev/null
@@ -1,49 +0,0 @@
-%\VignetteIndexEntry{Limma One Page Introduction}
-%\VignetteDepends{}
-%\VignetteKeywords{microarray linear model}
-%\VignettePackage{limma}
-\documentclass[12pt]{article}
-
-\textwidth=6.2in
-\textheight=8.5in
-\oddsidemargin=0.2in
-\evensidemargin=0.2in
-\headheight=0in
-\headsep=0in
-
-\begin{document}
-\title{Limma Package Introduction}
-\author{Gordon Smyth}
-\date{23 October 2004, Revised 21 October 2013}
-\maketitle
-
-Limma is an R package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression.
-Limma provides the ability to analyse comparisons between many RNA targets simultaneously in arbitrary complicated designed experiments.
-Empirical Bayesian methods are used to provide stable results even when the number of arrays is small.
-The normalization and data analysis functions are for two-color spotted microarrays.
-The linear model and differential expression functions apply to all microarray technologies including Affymetrix and other single-channel oligonucleotide platforms.
-
-The full Limma User's Guide is available as part of the online documentation.
-To reach the User's Guide you need to install the limma package.
-If you've installed the package and you're using Windows, type \texttt{library(limma)} at the R prompt then click on ``limma'' from the drop-down menu called ``Vignettes''.
-If you're not using Windows, you can type
-\begin{Schunk}
-\begin{Sinput}
-> library(limma)
-> limmaUsersGuide()
-\end{Sinput}
-\end{Schunk}
-or alternatively
-\begin{Schunk}
-\begin{Sinput}
-> help.start()
-\end{Sinput}
-\end{Schunk}
-and follow the links to the limma package help.
-
-\end{document}
-
-
-
-
-
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