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annotate CEMiTool.R @ 1:81bffdf16b71 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
author iuc
date Mon, 19 Aug 2024 10:47:14 +0000
parents 3f9ff31c88bb
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3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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1 # Load all required libraries
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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2 library(CEMiTool, quietly = TRUE, warn.conflicts = FALSE)
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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3 library(ggplot2, quietly = TRUE, warn.conflicts = FALSE)
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4 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
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5 # setup R error handling to go to stderr
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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6 options(
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
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7 show.error.messages = FALSE,
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8 error = function() {
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9 cat(geterrmessage(), file = stderr())
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10 q("no", 1, FALSE)
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11 }
0
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12 )
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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14 # we need that to not crash galaxy with an UTF8 error on German LC settings.
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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17 ################################################################################
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18 ### Input Processing
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19 ################################################################################
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21 # Collect arguments from command line
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22 args <- commandArgs(trailingOnly = TRUE)
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24 # Get options, using the spec as defined by the enclosed list.
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25 # Read the options from the default: commandArgs(TRUE).
1
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26 spec <- matrix(
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27 c(
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28 "expressionMatrix", "M", 1, "character",
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29 "sampleAnnotation", "A", 2, "character",
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30 "pathwayList", "P", 2, "character",
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31 "interactions", "I", 2, "character",
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32 "set_beta", "B", 1, "integer",
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33 "filter", "f", 1, "logical",
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34 "filter_pval", "i", 1, "numeric",
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35 "apply_vst", "a", 1, "logical",
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36 "n_genes", "n", 1, "integer",
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37 "eps", "e", 1, "numeric",
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38 "cor_method", "c", 1, "character",
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39 "cor_function", "y", 1, "character",
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40 "network_type", "x", 1, "character",
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41 "tom_type", "t", 1, "character",
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42 "merge_similar", "m", 1, "logical",
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43 "rank_method", "r", 1, "character",
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44 "min_ngen", "g", 1, "integer",
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45 "diss_thresh", "d", 1, "numeric",
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46 "center_func", "h", 1, "character",
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47 "ora_pval", "o", 1, "numeric",
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48 "gsea_scale", "l", 1, "logical",
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49 "gsea_min_size", "w", 1, "integer",
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50 "gsea_max_size", "z", 1, "integer",
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51 "sample_column_name", "v", 1, "character"
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52 ),
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53 byrow = TRUE, ncol = 4
0
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54 )
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56 opt <- getopt(spec)
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57 counts <- read.table(
1
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58 opt$expressionMatrix,
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59 header = TRUE,
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60 sep = "\t",
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61 strip.white = TRUE,
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62 stringsAsFactors = FALSE,
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63 check.names = FALSE
0
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64 )
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65
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66
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67 # Run CEMiTool
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68
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69 if (is.null(opt$sampleAnnotation)) {
1
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70 cem <- cemitool(
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71 counts,
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72 filter = opt$filter,
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73 filter_pval = opt$filter_pval,
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74 apply_vst = opt$apply_vst,
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75 n_genes = opt$n_genes,
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76 eps = opt$eps,
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77 cor_method = opt$cor_method,
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78 cor_function = opt$cor_function,
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79 network_type = opt$network_type,
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80 tom_type = opt$tom_type,
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81 merge_similar = opt$merge_similar,
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82 min_ngen = opt$min_ngen,
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83 diss_thresh = opt$diss_thresh,
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84 center_func = opt$center_func,
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85 verbose = TRUE,
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86 ora_pval = opt$ora_pval,
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87 set_beta = opt$set_beta
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88 )
0
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89 } else {
1
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90 annotation <- read.table(
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91 opt$sampleAnnotation,
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92 header = TRUE,
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93 sep = "\t",
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94 strip.white = TRUE,
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95 stringsAsFactors = FALSE,
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96 check.names = FALSE
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97 )
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98 cem <- cemitool(
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99 counts,
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100 annotation,
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101 filter = opt$filter,
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102 filter_pval = opt$filter_pval,
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103 apply_vst = opt$apply_vst,
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104 n_genes = opt$n_genes,
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105 eps = opt$eps,
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106 cor_method = opt$cor_method,
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107 cor_function = opt$cor_function,
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108 network_type = opt$network_type,
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109 tom_type = opt$tom_type,
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110 merge_similar = opt$merge_similar,
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111 min_ngen = opt$min_ngen,
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112 diss_thresh = opt$diss_thresh,
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113 center_func = opt$center_func,
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114 verbose = TRUE,
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115 ora_pval = opt$ora_pval,
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116 sample_name_column = opt$sample_column_name,
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117 class_column = "Class",
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118 order_by_class = TRUE
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119 )
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120 cem <- mod_gsea(
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121 cem,
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122 gsea_scale = opt$gsea_scale,
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123 gsea_min_size = opt$gsea_min_size,
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124 gsea_max_size = opt$gsea_max_size,
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125 rank_method = opt$rank_method
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126 )
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127 cem <- plot_gsea(cem)
0
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128 }
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129
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130 if (!is.null(opt$pathwayList)) {
1
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131 gmt_in <- read_gmt(opt$pathwayList)
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132 cem <- mod_ora(cem, gmt_in)
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133 cem <- plot_ora(cem)
0
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134 }
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135
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136 if (!is.null(opt$interactions)) {
1
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137 interactions <- read.table(
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138 opt$interactions,
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139 header = TRUE,
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140 sep = "\t",
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141 strip.white = TRUE,
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142 stringsAsFactors = FALSE,
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143 check.names = FALSE
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144 )
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145 interactions_data(cem) <- interactions # add interactions
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146 cem <- plot_interactions(cem)
0
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147 }
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148
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149 ## Write analysis results into files
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150 write_files(cem,
1
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151 directory = "./Tables",
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152 force = TRUE
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153 )
0
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154
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155 generate_report(cem)
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156
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157 save_plots(cem,
1
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158 value = "all",
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159 directory = "./Plots",
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160 force = TRUE
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161 )