Mercurial > repos > ppericard > viscorvar

annotate matCorAddVar_wrapper.R @ 0:d0b77b926863 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author ppericard
date Tue, 23 Jun 2020 19:57:35 -0400
parents
children e93350dc99f1
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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$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file")
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17 parser$add_argument('--block_Y_file', dest='block_Y_file', required=TRUE, help="Block Y filepath")
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18 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")
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19 parser$add_argument('--output_response_var', dest='output_response_var', required=TRUE, help="Output response variables file")
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20 parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file")
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22 args <- parser$parse_args()
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24 ## Print parameters
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25 print("Input RData:")
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26 print(args$input_rdata)
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27 print("Cutoff comp:")
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28 print(args$cutoff_comp)
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29 print("Variables of interest:")
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30 print(args$interest_var_file)
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31 print("Block Y file:")
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32 print(args$block_Y_file)
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33 print("Output RData:")
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34 print(args$output_rdata)
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35 print("Output Response variables:")
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36 print(args$output_response_var)
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37 print("Output Blocks combinations:")
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38 print(args$output_blocks_comb)
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39
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40 ## Loading libraries
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41 # source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R")
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42 install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL)
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43 suppressPackageStartupMessages(require(visCorVar))
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44 print("visCorVar has been loaded")
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45
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46 # R script call
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47 source_local <- function(fname)
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48 {
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49 argv <- commandArgs(trailingOnly = FALSE)
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50 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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51 source(paste(base_dir, fname, sep="/"))
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52 }
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53
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54 # Loading input Rdata file
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55 load(args$input_rdata)
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57 ncomp = mixomics_result$ncomp
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59 # Reading Block Y matrix
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60 print("Reading Block Y")
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61 mat_block_Y = read.table(args$block_Y_file, header=TRUE, row.names=1)
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62 print(mat_block_Y)
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64 response_var = colnames(mat_block_Y)
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66 print("response_var:")
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67 print(response_var)
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69 # Write response variables to output file
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70 invisible(lapply(response_var, write, file=args$output_response_var, append=TRUE, ncolumns=1))
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72 # Reading var of intereset file
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73 interest_var_vec = NULL
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74 if (args$interest_var_file != 'None') {
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75 interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]])
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76 }
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77
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78 #
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79 comp = 1:2
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80
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81 # Running main function
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82 res_matCorAddVar = matCorAddVar(res_block_splsda = mixomics_result,
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83 block_Y = mat_block_Y,
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84 cutoff_comp = args$cutoff_comp,
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85 var_interest = interest_var_vec,
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86 comp = comp)
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87
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88 #
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89 mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1
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90 mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2
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91 list_vec_index_block_select = res_matCorAddVar$list_vec_index_block_select
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92 list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks
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93 list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var
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94 res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest
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95
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96 #
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97 print("mat_cor_comp1:")
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98 print(mat_cor_comp1)
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99 print("mat_cor_comp2:")
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100 print(mat_cor_comp2)
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101 print("list_vec_index_block_select:")
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102 print(list_vec_index_block_select)
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103 print("list_vec_names_blocks:")
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104 print(list_vec_names_blocks)
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105 print("list_cor_comp_selected_var_resp_var:")
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106 print(list_cor_comp_selected_var_resp_var)
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107 print("res_compute_cor_var_interest:")
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108 print(res_compute_cor_var_interest)
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109
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110 # Write all possible blocks combinations to output file
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111 invisible(lapply(list_vec_names_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=","))
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112
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113 # Save all objects in Rdata output file
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114 save(res_matCorAddVar,
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115 file = args$output_rdata)