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comparison deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/densityPlot.R @ 10:6e573fd3c41b draft

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author yufei-luo
date Mon, 13 May 2013 10:06:30 -0400
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9:a03838a6eb54 10:6e573fd3c41b
1 # densityPlot
2 # density plot of all samples
3
4 # input : counts, target, projectName
5 # output : densplot (png)
6
7 # created Feb 7th, 2012
8 # modified April 30th, 2012
9 # Marie-Anges Dillies
10
11 densityPlot <- function( counts, group, OUT_densityPlotName, out = TRUE ){
12
13 if (out) png( file=OUT_densityPlotName )
14
15 couleurs <- as.integer( group ) + 1
16 ylim <- c(0, max(density(log2(counts)+1)$y)*1.5)
17 plot( density(log2(counts[,1])+1), main="Density of counts distribution", col=couleurs[1], ylim = ylim )
18 for (i in 2:ncol(counts))
19 lines( density(log2(counts[,i])+1), col=couleurs[i] )
20 legend( "topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 )
21
22 if (out) dev.off()
23 }