# HG changeset patch
# User moheydarian
# Date 1493312461 14400
# Node ID e75734b84e612f7b19b681d7d0bdb27b6f5f92b2
# Parent  c1cb330e162e83da79a73a9121f221dcb0a90c86
Uploaded

diff -r c1cb330e162e -r e75734b84e61 heatmap2.R
--- a/heatmap2.R	Thu Apr 27 13:00:52 2017 -0400
+++ b/heatmap2.R	Thu Apr 27 13:01:01 2017 -0400
@@ -22,6 +22,8 @@
   'transform', 'c', 2, 'character',
   'key', 'k', 2, 'character',
   'colorscheme', 'z', 2, 'character',
+  'cluster', 'b', 2, 'character',
+  'labels', 'a', 2, 'character',
   'output', 'o', 2, 'character'
   ), byrow=TRUE, ncol=4);
 
@@ -53,20 +55,42 @@
     }else{
 }
 
-if(options$colorscheme == "Default"){
+if(options$colorscheme == "whrd"){
   colorscale = colfunc <- colorRampPalette(c("white", "red"))
-} else {
+} else if(options$colorscheme == "whblu"){
+  colorscale = colfunc <- colorRampPalette(c("white", "blue"))
+}else if(options$colorscheme == "blwhre"){
   colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))
+}else{
 }
 
 
-hclust_fun = function(x) hclust(x, method="complete")
-dist_fun = function(x) dist(x, method="maximum")
+if(options$cluster== "Default"){
+  hclust_fun = function(x) hclust(x, method="complete")
+  dist_fun = function(x) dist(x, method="maximum")
+  clust = distfun=dist_fun, hclustfun=hclust_fun
+}else{
+  clust = NULL
+}
+
+if(options$labels== "both"){
+  labs = NULL
+}else if(options$labels== "rows"){
+  labs = labCol=FALSE
+}else if(options$labels== "columns"){
+  labs = labRow=FALSE
+}else if(options$labels== "none"){
+  labs = labRow=FALSE, labCol=FALSE
+} else{
+}
+
+
+
 
 pdf(file="Rplot.pdf")
 colorscale
 heatmap.2(linput,
-          distfun=dist_fun, hclustfun=hclust_fun, scale = "none",
-          col=colfunc(50), trace="none", density.info = "none",labRow=FALSE, margins=c(8,2),
+          clust, scale = options$scale,
+          col=colfunc(50), trace="none", density.info = "none", labs, margins=c(8,2),
           main = options$title, key.xlab= options$key, keysize=1)
 dev.off()