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- - - -Permalink - - +# Print options to see what is going on +cat("\n input: ",options$input) +cat("\n title: ",options$title) +cat("\n output: ",options$output) -
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- Galaxy-heatmap.2-wrapper/heatmap2.R -
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- - - 7db3994 - - Mar 14, 2017 - - - -
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+mat_input <- data.matrix(input[,2:ncol(input)]) - - -
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- 67 lines (49 sloc) - - 1.89 KB -
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# Setup R error handling to go to stderr
options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
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# We need to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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# Import library
library("getopt")
library("RColorBrewer")
library("gplots")
options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
# Take in trailing command line arguments
args <- commandArgs(trailingOnly = TRUE)
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# get options, using the spec as defined by the enclosed list.
# we read the options from the default: commandArgs(TRUE).
option_specification = matrix(c(
'input', 'i', 2, 'character',
'title', 't',2, 'character',
'transform', 'c', 2, 'character',
'keylabel', 'k',2, 'character',
'output', 'o', 2, 'character'
), byrow=TRUE, ncol=4);
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# Parse options
options = getopt(option_specification);
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# Print options to see what is going on
cat("\n input: ",options$input)
cat("\n title: ",options$title)
cat("\n output: ",options$output)
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input <- read.delim(options$input,sep='\t',header=TRUE)
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mat_input <- data.matrix(input[,2:ncol(input)])
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if(options$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{
}
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hclust_fun = function(x) hclust(x, method="complete")
dist_fun = function(x) dist(x, method="maximum")
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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()
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+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{ +} - -
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