view mixomics_plotindiv_script.R @ 1:e93350dc99f1 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"

#!/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, width=8, height=7)
mar = c(5, 5, 2, 8)
par(mar = mar)

# 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()