diff heatmap2.R @ 33:817f255101c6 draft

Uploaded

--- a/heatmap2.R	Thu Apr 27 15:33:38 2017 -0400
+++ b/heatmap2.R	Thu Apr 27 15:50:00 2017 -0400
@@ -43,6 +43,10 @@
 mat_input <- data.matrix(input[,2:ncol(input)])
 rownames(mat_input) <- input[,1]
 
+
+hclust_fun = function(x) hclust(x, method="complete")
+dist_fun = function(x) dist(x, method="maximum")
+
 if(options$transform == "none"){
     linput <- mat_input
 }else if(options$transform == "log2"){
@@ -67,15 +71,13 @@
 
 
 if(options$cluster== "Default"){
-  hclust_fun = function(x) hclust(x, method="complete")
-  dist_fun = function(x) dist(x, method="maximum")
   dclust = distfun=dist_fun
   hclust = hclustfun=hclust_fun
-  dend = NULL
+  dend = "both"
 }else{
   dclust = NULL
   hclust = NULL
-  dend = dendrogram = "none"
+  dend = "none"
 }
 
 if(options$labels== "both"){
@@ -99,7 +101,7 @@
 pdf(file="Rplot.pdf")
 colorscale
 heatmap.2(linput,
-          dclust, hclust, dend, scale = options$scale, labRow = rlabs, labCol = clabs,
+          dclust, hclust, dendrogram=dend, scale = options$scale, labRow = rlabs, labCol = clabs,
           col=colfunc(50), trace="none", density.info = "none", margins=c(8,2),
           main = options$title, key.xlab= options$key, keysize=1)
 dev.off()