--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_plotindiv_script.R	Fri May 17 05:00:22 2019 -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")
+
+## 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()
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