Mercurial > repos > ppericard > viscorvar

annotate circleCor_wrapper.R @ 1:e93350dc99f1 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author ppericard
date Thu, 15 Oct 2020 12:22:25 +0000
parents d0b77b926863
children
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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='Run the circleCor function')
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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('--blocks_vec', dest='blocks_vec', required=TRUE, help="Blocks vector")
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16 parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables")
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17 parser$add_argument('--x_min', dest='x_min', type='double', required=TRUE, help="X min")
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18 parser$add_argument('--x_max', dest='x_max', type='double', required=TRUE, help="X max")
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19 parser$add_argument('--y_min', dest='y_min', type='double', required=TRUE, help="Y min")
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20 parser$add_argument('--y_max', dest='y_max', type='double', required=TRUE, help="Y max")
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21 parser$add_argument('--output_var', dest='output_var', required=TRUE, help="Output variables file")
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22 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
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24 args <- parser$parse_args()
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26 ## Print parameters
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27 print("Input RData:")
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28 print(args$input_rdata)
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29 print("Blocks vector:")
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30 print(args$blocks_vec)
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31 print("Response variables:")
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32 print(args$responses_var)
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33 print("X min:")
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34 print(args$x_min)
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35 print("X max:")
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36 print(args$x_max)
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37 print("Y min:")
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38 print(args$y_min)
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39 print("Y max:")
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40 print(args$y_max)
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41 print("Output variables file:")
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42 print(args$output_var)
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43 print("Output PDF file:")
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44 print(args$output_pdf)
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45
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46 names_blocks = strsplit(args$blocks_vec, ",")[[1]]
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47 names_response_variables = strsplit(args$responses_var, ",")[[1]]
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48
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49 print("names_blocks:")
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50 print(names_blocks)
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51 print("names_response_variables:")
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52 print(names_response_variables)
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53
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54 ## Loading libraries
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55 # suppressPackageStartupMessages(require(ellipse))
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56 # suppressPackageStartupMessages(require(grDevices))
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57 # suppressPackageStartupMessages(require(RColorBrewer))
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58 # suppressPackageStartupMessages(require(mixOmics))
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59 ## Loading local functions
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60 # source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R")
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61 install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.5.tar.gz", repos=NULL)
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62 suppressPackageStartupMessages(require(visCorVar))
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63 print("visCorVar has been loaded")
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64
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65 # R script call
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66 source_local <- function(fname)
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67 {
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68 argv <- commandArgs(trailingOnly = FALSE)
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69 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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70 source(paste(base_dir, fname, sep="/"))
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71 }
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72
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73 # Loading input Rdata file
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74 # loads res_matCorAddVar object
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75 load(args$input_rdata)
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76
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77 mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1
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78 mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2
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79 cutoff_comp = res_matCorAddVar$cutoff_comp
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80 comp = res_matCorAddVar$comp
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81 list_vec_index_block_select = res_matCorAddVar$list_vec_index_block_select
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82 list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks
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83 list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var
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84 res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest
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85 res_block_splsda = res_matCorAddVar$res_block_splsda
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86
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87 #
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88 print("mat_cor_comp1:")
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89 print(mat_cor_comp1)
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90 print("mat_cor_comp2:")
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91 print(mat_cor_comp2)
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92 print("cutoff_comp:")
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93 print(cutoff_comp)
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94 print("comp:")
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95 print(comp)
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96 print("list_vec_index_block_select:")
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97 print(list_vec_index_block_select)
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98 print("list_vec_names_blocks:")
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99 print(list_vec_names_blocks)
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100 print("list_cor_comp_selected_var_resp_var:")
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101 print(list_cor_comp_selected_var_resp_var)
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102 print("res_compute_cor_var_interest:")
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103 print(res_compute_cor_var_interest)
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104
1
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105 # Open output pdf file
0
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106 pdf(args$output_pdf, width=8, height=7)
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107 mar = c(5, 5, 2, 8)
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108 par(mar = mar)
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109
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110 selected_variables = circleCor(list_dataframe_cor_comp_var_global = list_cor_comp_selected_var_resp_var,
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111 list_vec_index_block_select = list_vec_index_block_select,
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112 mat_cor_comp1 = mat_cor_comp1,
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113 mat_cor_comp2 = mat_cor_comp2,
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114 names_blocks = names_blocks,
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115 names_response_variables = names_response_variables,
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116 comp = comp,
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117 cutoff = 0.80,
0
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118 min.X = args$x_min,
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119 max.X = args$x_max,
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120 min.Y = args$y_min,
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121 max.Y = args$y_max,
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122 # vec_col = vec_col,
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123 rad.in = 0.5,
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124 cex = 0.7,
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125 cex_legend = 0.8,
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126 pos = c(1.2, 0),
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127 pch = 20)
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128
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129 dev.off()
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130
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131 write(selected_variables, file=args$output_var, ncolumns=1)