Mercurial > repos > ppericard > mixomics_blocksplsda

comparison mixomics_plotindiv_script.R @ 3:0a3c83f2197a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author ppericard
date Fri, 25 Oct 2019 07:10:59 -0400
parents bea08702ed51
children
comparison
equal deleted inserted replaced
2:655d1fbcd3e6 3:0a3c83f2197a
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