Mercurial > repos > ppericard > mixomics_blocksplsda

comparison 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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2:655d1fbcd3e6 3:0a3c83f2197a
1 #!/usr/bin/env Rscript
2
3 # Setup R error handling to go to stderr
4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
5
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")
8
9 ## Get parameters ##
10 suppressPackageStartupMessages(require(argparse))
11
12 parser <- ArgumentParser(description='Compute the matCorEtBlockSelect and addVariablesReponses functions')
13
14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
15 parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="")
16 parser$add_argument('--mat_block_Y_file', dest='mat_block_Y_file', required=TRUE, help="Matrix block Y filepath")
17 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")
18 parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file")
19
20 args <- parser$parse_args()
21
22 ## Print parameters
23 print("Input RData:")
24 print(args$input_rdata)
25 print("Cutoff comp:")
26 print(args$cutoff_comp)
27 print("Mat Block Y file:")
28 print(args$mat_block_Y_file)
29 print("Output RData:")
30 print(args$output_rdata)
31 print("Output Blocks combinations:")
32 print(args$output_blocks_comb)
33
34 ## Loading libraries
35 suppressPackageStartupMessages(require(mixOmics))
36
37 # R script call
38 source_local <- function(fname)
39 {
40 argv <- commandArgs(trailingOnly = FALSE)
41 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
42 source(paste(base_dir, fname, sep="/"))
43 }
44 ## Loading local functions
45 source_local("Integration_block_splsda_fonc.R")
46
47 load(args$input_rdata)
48
49 liste_matCorEtBlockSelect = matCorEtBlockSelect(res_block_splsda = mixomics_result,
50 cutoff_comp = args$cutoff_comp,
51 comp = 1:2)
52
53 mat_cor_comp1 = liste_matCorEtBlockSelect$mat_cor_comp1
54 mat_cor_comp2 = liste_matCorEtBlockSelect$mat_cor_comp2
55 dataframe_cor_comp_var_global = liste_matCorEtBlockSelect$dataframe_cor_comp_var_global
56 liste_vec_indice_blockSelect = liste_matCorEtBlockSelect$liste_vec_indice_blockSelect
57 liste_vec_blocks = liste_matCorEtBlockSelect$liste_vec_blocks
58
59 print("Mat cor comp1:")
60 print(mat_cor_comp1)
61 print("Mat cor comp2:")
62 print(mat_cor_comp2)
63 print("dataframe_cor_comp_var_global:")
64 print(dataframe_cor_comp_var_global)
65 print("liste_vec_indice_blockSelect:")
66 print(liste_vec_indice_blockSelect)
67 print("liste_vec_blocks:")
68 print(liste_vec_blocks)
69
70
71 lapply(liste_vec_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=",")
72
73
74 print("Reading Mat Block Y")
75 mat_block_Y = read.table(args$mat_block_Y_file, header=TRUE, row.names=1)
76 print(mat_block_Y)
77
78
79 liste_dataframe_cor_comp_var_global = addVariablesReponses(res_block_splsda = mixomics_result,
80 dataframe_cor_comp_var_global = dataframe_cor_comp_var_global,
81 liste_vec_indice_blockSelect = liste_vec_indice_blockSelect,
82 mat_block_Y = mat_block_Y)
83
84
85 save(mixomics_result,
86 liste_matCorEtBlockSelect,
87 mat_cor_comp1,
88 mat_cor_comp2,
89 dataframe_cor_comp_var_global,
90 liste_vec_indice_blockSelect,
91 liste_vec_blocks,
92 liste_dataframe_cor_comp_var_global,
93 file = args$output_rdata)