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-| - | # 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() | -