--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/densityPlot.R	Mon May 13 10:06:30 2013 -0400
@@ -0,0 +1,23 @@
+# densityPlot
+# density plot of all samples
+
+# input : counts, target, projectName
+# output : densplot (png)
+
+# created Feb 7th, 2012
+# modified April 30th, 2012
+# Marie-Anges Dillies
+
+densityPlot <- function( counts, group, OUT_densityPlotName, out = TRUE ){
+
+  if (out) png( file=OUT_densityPlotName )
+
+  couleurs <- as.integer( group ) + 1
+  ylim <- c(0, max(density(log2(counts)+1)$y)*1.5)
+  plot( density(log2(counts[,1])+1), main="Density of counts distribution", col=couleurs[1], ylim = ylim )
+  for (i in 2:ncol(counts))
+  	lines( density(log2(counts[,i])+1), col=couleurs[i] )
+  legend( "topright", as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 )
+
+  if (out) dev.off()
+}