diff heatmap2.R @ 30:175c65aca87a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap2.R	Thu Apr 27 15:25:28 2017 -0400
@@ -0,0 +1,105 @@
+# Setup R error handling to go to stderr
+options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
+
+# We need to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+
+# Import library
+library("getopt")
+library("RColorBrewer")
+library("gplots")
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+# Take in trailing command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+
+# get options, using the spec as defined by the enclosed list.
+# we read the options from the default: commandArgs(TRUE).
+option_specification = matrix(c(
+  'input', 'i', 2, 'character',
+  'title', 't', 2, 'character',
+  'transform', 'c', 2, 'character',
+  'key', 'k', 2, 'character',
+  'colorscheme', 'z', 2, 'character',
+  'cluster', 'b', 2, 'character',
+  'labels', 'a', 2, 'character',
+  'scale', 'd', 2, 'character',
+  'output', 'o', 2, 'character'
+  ), byrow=TRUE, ncol=4);
+
+# Parse options
+options = getopt(option_specification);
+
+
+
+# Print options to see what is going on
+cat("\n input: ",options$input)
+cat("\n title: ",options$title)
+cat("\n output: ",options$output)
+
+input <- read.delim(options$input,sep='\t',header=TRUE)
+
+mat_input <- data.matrix(input[,2:ncol(input)])
+rownames(mat_input) <- input[,1]
+
+if(options$transform == "none"){
+    linput <- mat_input
+}else if(options$transform == "log2"){
+    linput <- log2(mat_input)
+}else if(options$transform == "log2plus1"){
+    linput <- log2(mat_input+1)
+}else if(options$transform == "log10"){
+    linput <- log10(mat_input)
+}else if(options$transform == "log10plus1"){
+    linput <- log10(mat_input+1)
+    }else{
+}
+
+if(options$colorscheme == "whrd"){
+  colorscale = colfunc <- colorRampPalette(c("white", "red"))
+} else if(options$colorscheme == "whblu"){
+  colorscale = colfunc <- colorRampPalette(c("white", "blue"))
+}else if(options$colorscheme == "blwhre"){
+  colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))
+}else{
+}
+
+
+if(options$cluster== "Default"){
+  hclust_fun = function(x) hclust(x, method="complete")
+  dist_fun = function(x) dist(x, method="maximum")
+  dclust = distfun=dist_fun
+  hclust = hclustfun=hclust_fun
+  dend = NULL
+}else{
+  dclust = NULL
+  hclust = NULL
+  dend = "none"
+}
+
+if(options$labels== "both"){
+  rlabs = NULL
+  clabs = NULL
+}else if(options$labels== "rows"){
+  rlabs = NULL
+  clabs = FALSE
+}else if(options$labels== "columns"){
+  rlabs = FALSE
+  clabs = NULL
+}else if(options$labels== "none"){
+  rlabs = FALSE
+  clabs = FALSE
+} else{
+}
+
+
+
+
+pdf(file="Rplot.pdf")
+colorscale
+heatmap.2(linput,
+          dclust, hclust, dendrogram = dend, scale = options$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()