Mercurial > repos > ppericard > viscorvar

annotate mixomics_plotvar_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 ## Main Function ##
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11 suppressPackageStartupMessages(require(argparse))
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13 parser <- ArgumentParser(description='Run the mixOmics plotVar function')
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15 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
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16 parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend")
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17 parser$add_argument('--cutoff', dest='cutoff', type='double', required=TRUE, help="Cutoff (0..1)")
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18 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
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20 args <- parser$parse_args()
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22 ##
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23 print("Input RData:")
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24 print(args$input_rdata)
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25 print("Plot legend:")
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26 print(args$legend)
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27 print("Cutoff:")
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28 print(args$cutoff)
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29 print("Output PDF file:")
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30 print(args$output_pdf)
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32 # loading libraries
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33 suppressPackageStartupMessages(require(mixOmics))
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35 load(args$input_rdata)
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37 pdf(args$output_pdf, width=8, height=7)
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38 mar = c(5, 5, 2, 8)
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39 par(mar = mar)
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41 # plotVar(mixomics_result,
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42 # legend = args$legend,
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43 # cutoff = args$cutoff)
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45 for(k in 1:(length(mixomics_result$names[[3]])-1))
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46 {
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47 name_block = mixomics_result$names[[3]][k]
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49 # We're still continuing even if a graph is empty
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50 try(plotVar(mixomics_result,
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51 blocks = k,
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52 legend = args$legend,
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53 cutoff = args$cutoff),
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54 silent = FALSE)
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56 }
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58 dev.off()