Mercurial > repos > ppericard > mixomics_blocksplsda

annotate matCor_addVar_wrapper.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
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1 #!/usr/bin/env Rscript
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3 # Setup R error handling to go to stderr
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4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 ## Get parameters ##
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10 suppressPackageStartupMessages(require(argparse))
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12 parser <- ArgumentParser(description='Compute the matCorEtBlockSelect and addVariablesReponses functions')
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14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
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15 parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="")
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16 parser$add_argument('--mat_block_Y_file', dest='mat_block_Y_file', required=TRUE, help="Matrix block Y filepath")
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17 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")
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18 parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file")
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20 args <- parser$parse_args()
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22 ## Print parameters
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23 print("Input RData:")
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24 print(args$input_rdata)
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25 print("Cutoff comp:")
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26 print(args$cutoff_comp)
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27 print("Mat Block Y file:")
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28 print(args$mat_block_Y_file)
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29 print("Output RData:")
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30 print(args$output_rdata)
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31 print("Output Blocks combinations:")
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32 print(args$output_blocks_comb)
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34 ## Loading libraries
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35 suppressPackageStartupMessages(require(mixOmics))
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37 # R script call
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38 source_local <- function(fname)
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39 {
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40 argv <- commandArgs(trailingOnly = FALSE)
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41 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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42 source(paste(base_dir, fname, sep="/"))
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43 }
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44 ## Loading local functions
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45 source_local("Integration_block_splsda_fonc.R")
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47 load(args$input_rdata)
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49 liste_matCorEtBlockSelect = matCorEtBlockSelect(res_block_splsda = mixomics_result,
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50 cutoff_comp = args$cutoff_comp,
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51 comp = 1:2)
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52
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53 mat_cor_comp1 = liste_matCorEtBlockSelect$mat_cor_comp1
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54 mat_cor_comp2 = liste_matCorEtBlockSelect$mat_cor_comp2
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55 dataframe_cor_comp_var_global = liste_matCorEtBlockSelect$dataframe_cor_comp_var_global
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56 liste_vec_indice_blockSelect = liste_matCorEtBlockSelect$liste_vec_indice_blockSelect
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57 liste_vec_blocks = liste_matCorEtBlockSelect$liste_vec_blocks
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59 print("Mat cor comp1:")
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60 print(mat_cor_comp1)
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61 print("Mat cor comp2:")
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62 print(mat_cor_comp2)
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63 print("dataframe_cor_comp_var_global:")
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64 print(dataframe_cor_comp_var_global)
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65 print("liste_vec_indice_blockSelect:")
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66 print(liste_vec_indice_blockSelect)
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67 print("liste_vec_blocks:")
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68 print(liste_vec_blocks)
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71 lapply(liste_vec_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=",")
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74 print("Reading Mat Block Y")
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75 mat_block_Y = read.table(args$mat_block_Y_file, header=TRUE, row.names=1)
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76 print(mat_block_Y)
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79 liste_dataframe_cor_comp_var_global = addVariablesReponses(res_block_splsda = mixomics_result,
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80 dataframe_cor_comp_var_global = dataframe_cor_comp_var_global,
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81 liste_vec_indice_blockSelect = liste_vec_indice_blockSelect,
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82 mat_block_Y = mat_block_Y)
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83
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84
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85 save(mixomics_result,
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86 liste_matCorEtBlockSelect,
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87 mat_cor_comp1,
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88 mat_cor_comp2,
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89 dataframe_cor_comp_var_global,
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90 liste_vec_indice_blockSelect,
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91 liste_vec_blocks,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
92 liste_dataframe_cor_comp_var_global,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
93 file = args$output_rdata)