Mercurial > repos > ppericard > viscorvar
annotate mixomics_blocksplsda_script.R @ 1:e93350dc99f1 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author | ppericard |
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date | Thu, 15 Oct 2020 12:22:25 +0000 |
parents | d0b77b926863 |
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rev | line source |
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d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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1 #!/usr/bin/env Rscript |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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2 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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3 # Setup R error handling to go to stderr |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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5 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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8 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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9 ## Get parameters ## |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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10 suppressPackageStartupMessages(require(argparse)) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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11 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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12 parser <- ArgumentParser(description='Run the mixOmics block.splsda function') |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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13 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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14 parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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15 help="Block name + nb variables to select + data matrix file + variables metadata file") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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16 parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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17 help="Samples metadata file") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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18 parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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19 default=0, help="Sample description column number") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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20 parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2, |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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21 help="Number of components to include in the model") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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22 parser$add_argument('--correlation', dest='correlation', action="store_true", |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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23 help="Add correlation between all blocks") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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24 parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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25 parser$add_argument('--mode', dest='mode', default="regression", help="Mode") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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26 parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100, |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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27 help="Maximum number of iterations") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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28 parser$add_argument('--scale', dest='scale', action="store_true", |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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29 help="Each block is standardized to zero means and unit variances") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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30 parser$add_argument('--check_missing_values', dest='check_missing_values', action="store_true", |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
parents:
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31 help="Check for missing values and raise an error") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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32 parser$add_argument('--init', dest='init', default="svd", |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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33 help="Init (svd or svd.single)") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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34 parser$add_argument('--tol', dest='tol', type='double', default=1e-06, |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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35 help="Convergence stopping value") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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36 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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37 help="Should be set in particular for data with many zero values") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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38 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file") |
1
e93350dc99f1
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
ppericard
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39 # parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file") |
0
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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40 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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41 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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42 args <- parser$parse_args() |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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43 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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44 ## Print parameters |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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45 print("Blocks:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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46 print(args$blocks_list) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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47 print("Sample metadata file:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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48 print(args$sample_metadata_in) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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49 print("Sample description column number:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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50 print(args$sample_description_col) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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51 print("Number of components:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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52 print(args$ncomp) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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53 print("Compute correlation between all blocks:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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54 print(args$correlation) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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55 print("Scheme:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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56 print(args$scheme) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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57 print("Mode:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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58 print(args$mode) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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59 print("Max nb of iterations:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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60 print(args$maxiter) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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61 print("Scale:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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62 print(args$scale) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
ppericard
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63 print("Check for missing values:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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64 print(args$check_missing_values) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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65 print("Tol:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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66 print(args$tol) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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67 print("near.zero.var:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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68 print(args$nearzerovar) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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69 print("Output Rdata file:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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70 print(args$rdata_out) |
1
e93350dc99f1
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
ppericard
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71 # print("Output sample metadata file:") |
e93350dc99f1
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
ppericard
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72 # print(args$sample_metadata_out) |
0
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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73 print("Output variable metadata directory:") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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74 print(args$variable_metadata_outdir) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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75 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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76 ## Loading libraries |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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77 suppressPackageStartupMessages(require(mixOmics)) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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78 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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79 ## Read sample metadata file and set description factor matrix |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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80 sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1) |
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81 sample_metadata_names <- row.names(sample_metadata) |
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82 # print(sample_metadata_names) |
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83 |
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84 # print("Sample metadata matrix:") |
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85 # print(head(sample_metadata)) |
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86 |
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87 description_column <- ncol(sample_metadata) |
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88 if(args$sample_description_col > 0) |
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89 { |
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90 description_column <- args$sample_description_col |
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91 } |
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92 |
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93 Y <- factor(sample_metadata[[description_column]]) |
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94 |
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95 print("Y factor matrix:") |
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96 print(Y) |
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97 |
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98 ## Read and prepare block datasets |
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99 list_X <- c() |
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100 keepX <- c() |
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101 |
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102 for(i in 1:nrow(args$blocks_list)) |
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103 { |
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104 # Read block input parameters |
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105 block_name <- args$blocks_list[i,1] |
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106 block_keep <- strtoi(args$blocks_list[i,2]) |
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107 block_data_matrix_filename <- args$blocks_list[i,3] |
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108 # block_meta_var <- args$blocks_list[i,4] |
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109 |
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110 print(sprintf("Processing block %s", block_name)) |
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111 |
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112 # Store block data matrices |
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113 block_data_matrix <- t(read.table(block_data_matrix_filename, sep='\t', header=TRUE, row.names=1)) # transpose the matrix so that the samples become rows and the variables become columns |
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114 block_data_matrix_names <- row.names(block_data_matrix) |
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115 # print(block_data_matrix_names) |
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116 |
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117 if(!identical(sample_metadata_names, block_data_matrix_names)) |
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118 { |
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119 stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix") |
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120 } |
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121 |
1
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122 if(any(is.na(block_data_matrix))) |
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123 { |
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124 stop(sprintf("Block %s contains missing values. We recommend not to perform data integration with missing values. If you want to force run, change the advanced parameter 'Check for missing values' to 'No'.", block_name)) |
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125 } |
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126 |
0
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127 list_X[[block_name]] <- block_data_matrix |
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128 |
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129 # Set the nb of variables to keep |
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130 nb_variables = ncol(list_X[[block_name]]) |
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131 if(block_keep > 0) |
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132 { |
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133 keepX[[block_name]] <- rep(block_keep, args$ncomp) |
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134 } |
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135 else |
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136 { |
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137 keepX[[block_name]] <- rep(nb_variables, args$ncomp) |
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138 } |
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139 print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep)) |
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140 } |
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141 |
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142 # print(list_X) |
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143 |
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144 ## Generate design matrix |
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145 block_nb <- nrow(args$blocks_list) |
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146 |
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147 design <- matrix(0, nrow = block_nb, ncol = block_nb) |
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148 |
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149 if(args$correlation) |
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150 { |
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151 design <- matrix(1, nrow = block_nb, ncol = block_nb) |
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152 diag(design) <- 0 |
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153 } |
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154 |
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155 # print("Design matrix:") |
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156 # print(design) |
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157 |
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158 ################### |
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159 ## Main function ## |
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160 ################### |
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161 |
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162 mixomics_result <- block.splsda(X = list_X, |
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163 Y = Y, |
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164 ncomp = args$ncomp, |
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165 keepX = keepX, |
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166 design = design, |
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167 scheme = args$scheme, |
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168 mode = args$mode, |
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169 scale = args$scale, |
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170 init = args$init, |
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171 tol = args$tol, |
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172 max.iter = args$maxiter, |
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173 near.zero.var = args$nearzerovar, |
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174 all.outputs = TRUE) |
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175 |
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176 print("Block.splsda object:") |
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177 print(mixomics_result) |
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178 print(attributes(mixomics_result)) |
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179 |
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180 ## Save output Rdata file |
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181 save(mixomics_result, file=args$rdata_out) |
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182 |
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183 # R script call |
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184 source_local <- function(fname) |
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185 { |
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186 argv <- commandArgs(trailingOnly = FALSE) |
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187 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) |
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188 source(paste(base_dir, fname, sep="/")) |
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189 } |
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190 |
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191 # Load library |
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192 source_local("additional_functions_block_splsda.R") |
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193 |
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194 |
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195 |
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196 list_union_selected_block_variables = unionSelectBlockVariables(mixomics_result) |
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197 |
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198 ## Save output sample metadata file |
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199 # print("Block.splsda variates:") |
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200 # print(mixomics_result$variates) |
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201 |
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202 # for(block_name in names(mixomics_result$variates)) |
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203 # { |
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204 # # print(block_name) |
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205 # # print(mixomics_result$variates[[block_name]]) |
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206 |
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207 # # Format the column names to add the block name and replace spaces |
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208 # colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_") |
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209 # # print(mixomics_result$variates[[block_name]]) |
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210 |
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211 # # Append the new columns to the sample metadata matrix |
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212 # sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]]) |
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213 # } |
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214 |
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215 # print(sample_metadata) |
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216 |
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217 # write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) |
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218 |
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219 ## Save output variable metadata files in output directory |
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220 # print("Block.splsda loadings:") |
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221 # print(mixomics_result$loadings) |
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222 |
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223 for(i in 1:nrow(args$blocks_list)) |
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224 { |
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225 # Read again block input parameters |
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226 block_name <- args$blocks_list[i,1] |
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227 # block_keep <- strtoi(args$blocks_list[i,2]) |
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228 # block_data_matrix_filename <- args$blocks_list[i,3] |
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229 block_meta_var <- args$blocks_list[i,4] |
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230 |
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231 print(sprintf("Saving block %s output metavar", block_name)) |
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232 |
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233 |
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234 meta_variable <- list_union_selected_block_variables[[i]] |
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235 colnames(meta_variable) <- "block.splsda_var_select" |
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236 |
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237 # meta_variable <- mixomics_result$loadings[[block_name]] |
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238 # print(head(meta_variable)) |
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239 |
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240 # Format the column names to add the block name and replace spaces |
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241 # colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_") |
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242 |
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243 # Read input block variable metadata files if provided (optional) |
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244 if(block_meta_var != "None") |
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245 { |
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246 input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1) |
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247 # print(head(input_meta_variable)) |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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248 |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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249 # Append the new columns to the variable metadata matrix |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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250 meta_variable <- cbind2(input_meta_variable, meta_variable) |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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251 } |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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252 |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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253 # print(head(meta_variable)) |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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254 |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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255 block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="") |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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256 write.table(meta_variable, file = paste(args$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
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257 } |