Mercurial > repos > ppericard > viscorvar
comparison mixomics_plotindiv_script.R @ 0:d0b77b926863 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author | ppericard |
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date | Tue, 23 Jun 2020 19:57:35 -0400 |
parents | |
children | e93350dc99f1 |
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-1:000000000000 | 0:d0b77b926863 |
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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 ## Get parameters ## | |
10 suppressPackageStartupMessages(require(argparse)) | |
11 | |
12 parser <- ArgumentParser(description='Run the mixOmics plotIndiv function') | |
13 | |
14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") | |
15 parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") | |
16 parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") | |
17 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") | |
18 | |
19 args <- parser$parse_args() | |
20 | |
21 ## Print parameters | |
22 print("Input RData:") | |
23 print(args$input_rdata) | |
24 print("Plot legend:") | |
25 print(args$legend) | |
26 print("Plot ellipse plots:") | |
27 print(args$ellipse) | |
28 print("Output PDF file:") | |
29 print(args$output_pdf) | |
30 | |
31 # loading libraries | |
32 suppressPackageStartupMessages(require(mixOmics)) | |
33 | |
34 load(args$input_rdata) | |
35 | |
36 pdf(args$output_pdf) | |
37 | |
38 # plotIndiv(mixomics_result, | |
39 # legend = args$legend, | |
40 # ellipse = args$ellipse) | |
41 | |
42 for(k in 1:(length(mixomics_result$names[[3]])-1)) | |
43 { | |
44 name_block = mixomics_result$names[[3]][k] | |
45 | |
46 try(plotIndiv(mixomics_result, | |
47 blocks = k, | |
48 legend = args$legend, | |
49 ellipse = args$ellipse), | |
50 silent = FALSE) | |
51 } | |
52 | |
53 dev.off() |