Mercurial > repos > ppericard > mixomics_blocksplsda
view mixomics_plotindiv_script.R @ 1:6595c17673cb draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
author | ppericard |
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date | Wed, 12 Jun 2019 11:22:33 -0400 |
parents | bea08702ed51 |
children | 0a3c83f2197a |
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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 plotIndiv 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$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") parser$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$legend) print("Plot ellipse plots:") print(args$ellipse) print("Output PDF file:") print(args$output_pdf) # loading libraries suppressPackageStartupMessages(require(mixOmics)) load(args$input_rdata) pdf(args$output_pdf) plotIndiv(mixomics_result, legend = args$legend, ellipse = args$ellipse) for(k in 1:(length(mixomics_result$names[[3]])-1)) { name_block = mixomics_result$names[[3]][k] plotIndiv(mixomics_result, blocks = k, legend = args$legend, ellipse = args$ellipse) } dev.off()