changeset 29:eecf7fddf834 draft

Deleted selected files

--- a/heatmap2.R	Thu Apr 27 15:10:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
-# 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()