Mercurial > repos > ppericard > mixomics_blocksplsda

annotate mixomics_plotindiv_script.R @ 4:b0ab97ffc2a1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
author ppericard
date Mon, 09 Mar 2020 11:53:32 -0400
parents 0a3c83f2197a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
1 #!/usr/bin/env Rscript
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
2
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
3 # Setup R error handling to go to stderr
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
5
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
8
3
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents: 0
diff changeset
9 ## Get parameters ##
0
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
10 suppressPackageStartupMessages(require(argparse))
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
11
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
12 parser <- ArgumentParser(description='Run the mixOmics plotIndiv function')
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
13
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
15 parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
16 parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
17 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
18
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
19 args <- parser$parse_args()
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
20
3
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents: 0
diff changeset
21 ## Print parameters
0
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
22 print("Input RData:")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
23 print(args$input_rdata)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
24 print("Plot legend:")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
25 print(args$legend)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
26 print("Plot ellipse plots:")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
27 print(args$ellipse)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
28 print("Output PDF file:")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
29 print(args$output_pdf)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
30
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
31 # loading libraries
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
32 suppressPackageStartupMessages(require(mixOmics))
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
33
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
34 load(args$input_rdata)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
35
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
36 pdf(args$output_pdf)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
37
3
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents: 0
diff changeset
38 # plotIndiv(mixomics_result,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents: 0
diff changeset
39 # legend = args$legend,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents: 0
diff changeset
40 # ellipse = args$ellipse)
0
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
41
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
42 for(k in 1:(length(mixomics_result$names[[3]])-1))
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
43 {
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
44 name_block = mixomics_result$names[[3]][k]
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
45
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
46 plotIndiv(mixomics_result,
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
47 blocks = k,
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
48 legend = args$legend,
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
49 ellipse = args$ellipse)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
50 }
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
51
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff changeset
52 dev.off()