Mercurial > repos > ppericard > viscorvar

annotate mixomics_plotindiv_script.R @ 1:e93350dc99f1 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author ppericard
date Thu, 15 Oct 2020 12:22:25 +0000
parents d0b77b926863
children
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1 #!/usr/bin/env Rscript
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3 # Setup R error handling to go to stderr
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4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 ## Get parameters ##
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10 suppressPackageStartupMessages(require(argparse))
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12 parser <- ArgumentParser(description='Run the mixOmics plotIndiv function')
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14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
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15 parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend")
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16 parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots")
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17 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
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19 args <- parser$parse_args()
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21 ## Print parameters
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22 print("Input RData:")
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23 print(args$input_rdata)
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24 print("Plot legend:")
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25 print(args$legend)
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26 print("Plot ellipse plots:")
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27 print(args$ellipse)
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28 print("Output PDF file:")
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29 print(args$output_pdf)
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31 # loading libraries
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32 suppressPackageStartupMessages(require(mixOmics))
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34 load(args$input_rdata)
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36 pdf(args$output_pdf, width=8, height=7)
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37 mar = c(5, 5, 2, 8)
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38 par(mar = mar)
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40 # plotIndiv(mixomics_result,
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41 # legend = args$legend,
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42 # ellipse = args$ellipse)
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44 for(k in 1:(length(mixomics_result$names[[3]])-1))
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45 {
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46 name_block = mixomics_result$names[[3]][k]
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48 try(plotIndiv(mixomics_result,
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49 blocks = k,
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50 legend = args$legend,
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51 ellipse = args$ellipse),
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52 silent = FALSE)
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53 }
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55 dev.off()