Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

diff deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/MAplotDE.R @ 10:6e573fd3c41b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author yufei-luo
date Mon, 13 May 2013 10:06:30 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/MAplotDE.R	Mon May 13 10:06:30 2013 -0400
@@ -0,0 +1,17 @@
+# Marie-Anges Dillies
+# MAplotDE
+# MAplot of DE genes
+
+# input : res, alpha,OUT_MAplotDEName 
+# output : MAplot (png)
+
+MAplotDE <- function( res, alpha, OUT_MAplotDEName, out = TRUE ){
+
+ 	if (out) png( file=OUT_MAplotDEName )
+  
+ 	plot( res$baseMean, res$log2FoldChange, pch=".", xlab="Mean expression", ylab="log2FC", main="",
+  		log="x", col=ifelse(res$padj < alpha, "red", "black") )
+	abline(h=0, col="red")
+
+  	if (out) dev.off()
+}