--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/majSequence.R	Mon May 13 10:06:30 2013 -0400
@@ -0,0 +1,26 @@
+# majSequence
+# compute proportion of reads associated with most expressed sequence
+
+# input : counts, target, projectName
+# output : barplot, % associated with majority gene
+
+# created Feb 7th, 2012
+# modified Feb 20th, 2012
+# modified April 30th, 2012
+# Marie-Agnes Dillies
+
+
+majSequence <- function( counts, group, OUT_majSequenceName, out = T, position = "topright" ){
+
+  if (out) png( file=OUT_majSequenceName )
+
+  maj <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; x[1]*100/sum(x)})
+  seqname <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; names(x)[1]})
+
+  x <- barplot( maj, col=as.integer(group)+1, main = "Proportion of reads from most expressed gene", 
+		ylim = c(0, max(maj)*1.2), cex.main=0.8 )
+  for (i in 1:length(seqname)) text( x[i], maj[i]/2, seqname[i], cex=0.8, srt=90, adj=0)
+  legend( position, as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 )
+
+  if (out) dev.off()
+}