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commit c310b4a96f437ece5329b3d2248bb1c77ba4a94c Author: Andreas Tille <[email protected]> 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} - - - - - -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
