Mercurial > repos > ppericard > mixomics_blocksplsda
comparison mixomics_plotindiv_script.R @ 0:bea08702ed51 draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
| author | ppericard |
|---|---|
| date | Fri, 17 May 2019 05:00:22 -0400 |
| parents | |
| children | 0a3c83f2197a |
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| -1:000000000000 | 0:bea08702ed51 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 # Setup R error handling to go to stderr | |
| 4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 5 | |
| 6 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
| 7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| 8 | |
| 9 ## Main Function ## | |
| 10 | |
| 11 suppressPackageStartupMessages(require(argparse)) | |
| 12 | |
| 13 parser <- ArgumentParser(description='Run the mixOmics plotIndiv function') | |
| 14 | |
| 15 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") | |
| 16 parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") | |
| 17 parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") | |
| 18 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") | |
| 19 | |
| 20 args <- parser$parse_args() | |
| 21 | |
| 22 ## | |
| 23 print("Input RData:") | |
| 24 print(args$input_rdata) | |
| 25 print("Plot legend:") | |
| 26 print(args$legend) | |
| 27 print("Plot ellipse plots:") | |
| 28 print(args$ellipse) | |
| 29 print("Output PDF file:") | |
| 30 print(args$output_pdf) | |
| 31 | |
| 32 # loading libraries | |
| 33 suppressPackageStartupMessages(require(mixOmics)) | |
| 34 | |
| 35 load(args$input_rdata) | |
| 36 | |
| 37 pdf(args$output_pdf) | |
| 38 | |
| 39 plotIndiv(mixomics_result, | |
| 40 legend = args$legend, | |
| 41 ellipse = args$ellipse) | |
| 42 | |
| 43 for(k in 1:(length(mixomics_result$names[[3]])-1)) | |
| 44 { | |
| 45 name_block = mixomics_result$names[[3]][k] | |
| 46 | |
| 47 plotIndiv(mixomics_result, | |
| 48 blocks = k, | |
| 49 legend = args$legend, | |
| 50 ellipse = args$ellipse) | |
| 51 } | |
| 52 | |
| 53 dev.off() |