Mercurial > repos > ppericard > mixomics_blocksplsda
comparison mixomics_plotindiv_script.R @ 3:0a3c83f2197a draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author | ppericard |
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date | Fri, 25 Oct 2019 07:10:59 -0400 |
parents | bea08702ed51 |
children |
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2:655d1fbcd3e6 | 3:0a3c83f2197a |
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4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | 4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
5 | 5 |
6 # we need that to not crash galaxy with an UTF8 error on German LC settings. | 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") | 7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
8 | 8 |
9 ## Main Function ## | 9 ## Get parameters ## |
10 | |
11 suppressPackageStartupMessages(require(argparse)) | 10 suppressPackageStartupMessages(require(argparse)) |
12 | 11 |
13 parser <- ArgumentParser(description='Run the mixOmics plotIndiv function') | 12 parser <- ArgumentParser(description='Run the mixOmics plotIndiv function') |
14 | 13 |
15 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") | 14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") |
17 parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") | 16 parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") |
18 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") | 17 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") |
19 | 18 |
20 args <- parser$parse_args() | 19 args <- parser$parse_args() |
21 | 20 |
22 ## | 21 ## Print parameters |
23 print("Input RData:") | 22 print("Input RData:") |
24 print(args$input_rdata) | 23 print(args$input_rdata) |
25 print("Plot legend:") | 24 print("Plot legend:") |
26 print(args$legend) | 25 print(args$legend) |
27 print("Plot ellipse plots:") | 26 print("Plot ellipse plots:") |
34 | 33 |
35 load(args$input_rdata) | 34 load(args$input_rdata) |
36 | 35 |
37 pdf(args$output_pdf) | 36 pdf(args$output_pdf) |
38 | 37 |
39 plotIndiv(mixomics_result, | 38 # plotIndiv(mixomics_result, |
40 legend = args$legend, | 39 # legend = args$legend, |
41 ellipse = args$ellipse) | 40 # ellipse = args$ellipse) |
42 | 41 |
43 for(k in 1:(length(mixomics_result$names[[3]])-1)) | 42 for(k in 1:(length(mixomics_result$names[[3]])-1)) |
44 { | 43 { |
45 name_block = mixomics_result$names[[3]][k] | 44 name_block = mixomics_result$names[[3]][k] |
46 | 45 |