Mercurial > repos > ppericard > viscorvar
diff mixomics_plotindiv_script.R @ 0:d0b77b926863 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author | ppericard |
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date | Tue, 23 Jun 2020 19:57:35 -0400 |
parents | |
children | e93350dc99f1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotindiv_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,53 @@ +#!/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") + +## Get parameters ## +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$parse_args() + +## Print parameters +print("Input RData:") +print(args$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$names[[3]][k] + + try(plotIndiv(mixomics_result, + blocks = k, + legend = args$legend, + ellipse = args$ellipse), + silent = FALSE) +} + +dev.off() \ No newline at end of file