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diff mytools/alignvis.r @ 9:87eb5c5ddfe9

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author xuebing
date Fri, 09 Mar 2012 20:01:43 -0500
parents f0dc65e7f6c0
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/alignvis.r	Fri Mar 09 20:01:43 2012 -0500
@@ -0,0 +1,8 @@
+args <- commandArgs(TRUE)
+x <- read.table(args[1])
+pdf(args[2])
+#visualize the profile with heatmap 
+srt <- sort(x[,2],index.return=T) # sort by total number of reads
+image(-t(log(as.matrix(x[srt$ix[1:nrow(x)],3:ncol(x)],nc=ncol(x)-2))),col=gray.colors(100))
+dev.off()
+