+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Permalink
+
+
+
+
+
+
+
+
+
+
+
+
+ 
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+| + | # 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', | +
| + | 'keylabel', 'k',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)]) | +
| + | + | +
| + | + | +
| + | 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$transform == "log10plus1"){ | +
| + | linput <- log10(mat_input+1) | +
| + | }else{ | +
| + | } | +
| + | + | +
| + | + | +
| + | + | +
| + | hclust_fun = function(x) hclust(x, method="complete") | +
| + | dist_fun = function(x) dist(x, method="maximum") | +
| + | + | +
| + | pdf(file="Rplot.pdf") | +
| + | colfunc <- colorRampPalette(c("white", "red")) | +
| + | heatmap.2(linput, | +
| + | distfun=dist_fun, hclustfun=hclust_fun, scale = "none", | +
| + | col=colfunc(50), trace="none", density.info = "none",labRow=FALSE, margins=c(8,2), | +
| + | main = options$title, key.xlab= options$keylabel, keysize=1) | +
| + | dev.off() | +