Mercurial > repos > ppericard > viscorvar
view mixomics_plotvar_script.R @ 1:e93350dc99f1 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author | ppericard |
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date | Thu, 15 Oct 2020 12:22:25 +0000 |
parents | d0b77b926863 |
children |
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#!/usr/bin/env Rscript # 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 that to not crash galaxy with an UTF8 error on German LC settings. loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") ## Main Function ## suppressPackageStartupMessages(require(argparse)) parser <- ArgumentParser(description='Run the mixOmics plotVar function') parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") parser$add_argument('--cutoff', dest='cutoff', type='double', required=TRUE, help="Cutoff (0..1)") parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") args <- parser$parse_args() ## print("Input RData:") print(args$input_rdata) print("Plot legend:") print(args$legend) print("Cutoff:") print(args$cutoff) print("Output PDF file:") print(args$output_pdf) # loading libraries suppressPackageStartupMessages(require(mixOmics)) load(args$input_rdata) pdf(args$output_pdf, width=8, height=7) mar = c(5, 5, 2, 8) par(mar = mar) # plotVar(mixomics_result, # legend = args$legend, # cutoff = args$cutoff) for(k in 1:(length(mixomics_result$names[[3]])-1)) { name_block = mixomics_result$names[[3]][k] # We're still continuing even if a graph is empty try(plotVar(mixomics_result, blocks = k, legend = args$legend, cutoff = args$cutoff), silent = FALSE) } dev.off()