Mercurial > repos > moheydarian > heatmap2

changeset 25:43f627dc005e draft

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Uploaded
author moheydarian
date Thu, 27 Apr 2017 14:54:06 -0400
parents 5bae1e1fcec3
children b9cb6b047ff8
files heatmap2.R
diffstat 1 files changed, 5 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/heatmap2.R	Thu Apr 27 14:06:41 2017 -0400
+++ b/heatmap2.R	Thu Apr 27 14:54:06 2017 -0400
@@ -40,8 +40,8 @@
 
 input <- read.delim(options$input,sep='\t',header=TRUE)
 
-mat_input <- data.matrix(input)  
-
+mat_input <- data.matrix(input[,2:ncol(input)])
+rownames(mat_input) <- input[,1]
 
 if(options$transform == "none"){
     linput <- mat_input
@@ -71,12 +71,11 @@
   dist_fun = function(x) dist(x, method="maximum")
   dclust = distfun=dist_fun
   hclust = hclustfun=hclust_fun
+  dend = NULL
 }else{
   dclust = NULL
   hclust = NULL
-  rowd = Rowv = NULL
-  cold = Colv = NULL
-  dend = dendrogram = "none"
+  dend = dendrogram="none"
 }
 
 if(options$labels== "both"){
@@ -100,7 +99,7 @@
 pdf(file="Rplot.pdf")
 colorscale
 heatmap.2(linput,
-          dclust, hclust, rowd, cold, scale = options$scale, rlabs, clabs,
+          dclust, hclust, dend, scale = options$scale, rlabs, clabs,
           col=colfunc(50), trace="none", density.info = "none", margins=c(8,2),
           main = options$title, key.xlab= options$key, keysize=1)
 dev.off()