Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov_wrapper.R @ 1:0c2ad44b6c9c draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
author eschen42
date Sun, 22 Oct 2017 18:47:57 -0400
parents 23f9fad4edfc
children e03582f26617
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1 #!/usr/bin/env Rscript
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3 # This script assumes that it is being executed in a current working directory containing the following files:
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4 # - w4mcorcov_lib.R
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5 # - w4mcorcov_input.R
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6 # - w4mcorcov_calc.R
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8 ## constants
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9 ##----------
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11 modNamC <- "w4mcorcov" ## module name
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13 topEnvC <- environment()
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14 nl <- "\n"
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16 ## options
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17 ##--------
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19 strAsFacL <- options()$stringsAsFactors
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20 options(stringsAsFactors = FALSE)
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22 ## subroutines
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23 ##----------
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25 source("w4mcorcov_lib.R")
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26 source("w4mcorcov_util.R")
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27 source("w4mcorcov_input.R")
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28 source("w4mcorcov_salience.R")
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29 source("w4mcorcov_calc.R")
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30 source("w4mcorcov_output.R")
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32 ## log file
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33 ##---------
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35 my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))}
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36 my_fatal <- function(x, ...) {
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37 my_log("ERROR: ", x, ...)
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38 quit(save = "no", status = 11, runLast = TRUE)
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39 }
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41 my_log("Start of the '", modNamC, "' Galaxy module call: ")
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44 ########
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45 # MAIN #
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46 ########
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48 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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49 my_env <- new.env()
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51 ##------------------------------
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52 ## Initializing
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53 ##------------------------------
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54
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55 ## arguments
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56 ##----------
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57
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58 # files
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59
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60 my_env$dataMatrix_in <- as.character(argVc["dataMatrix_in"])
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61 my_env$sampleMetadata_in <- as.character(argVc["sampleMetadata_in"])
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62 my_env$variableMetadata_in <- as.character(argVc["variableMetadata_in"])
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63 my_env$contrast_detail <- as.character(argVc["contrast_detail"])
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64 my_env$contrast_corcov <- as.character(argVc["contrast_corcov"])
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65 my_env$contrast_salience <- as.character(argVc["contrast_salience"])
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66 # print(sprintf("contrast_salience: %s", my_env$contrast_salience))
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67
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68 # other parameters
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69
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70 my_env$tesC <- as.character(argVc["tesC"])
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71 my_env$facC <- as.character(argVc["facC"])
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72 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"])
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73 my_env$levCSV <- as.character(argVc["levCSV"])
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74 my_env$matchingC <- as.character(argVc["matchingC"])
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75 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'
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77 label_features <- my_env$labelFeatures
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78 labelfeatures_check <- TRUE
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79 if ( is.na(label_features) ) {
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80 labelfeatures_check <- FALSE
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81 } else if ( is.null(label_features) ) {
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82 labelfeatures_check <- FALSE
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83 } else if (label_features != "ALL") {
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84 if ( is.na(as.numeric(label_features)) )
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85 labelfeatures_check <- FALSE
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86 else if ( as.numeric(label_features) < 0 )
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87 labelfeatures_check <- FALSE
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88 }
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diff changeset
89 if ( !labelfeatures_check ) {
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diff changeset
90 my_log("invalid argument: labelFeatures")
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diff changeset
91 print(label_features)
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92 quit(save = "no", status = 10, runLast = TRUE)
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diff changeset
93 }
0
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94
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95 tsv_action_factory <- function(file, colnames, append) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
96 return (
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97 function(tsv) {
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98 write.table(
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99 x = tsv
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100 , file = file
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101 , sep = "\t"
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102 , quote = FALSE
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103 , row.names = FALSE
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104 , col.names = colnames
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105 , append = append
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106 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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107 }
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108 )
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109 }
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110
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111 corcov_tsv_colnames <- TRUE
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112 corcov_tsv_append <- FALSE
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113 corcov_tsv_action <- function(tsv) {
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114 tsv_action_factory(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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115 file = my_env$contrast_corcov
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116 , colnames = corcov_tsv_colnames
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117 , append = corcov_tsv_append
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118 )(tsv)
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119 corcov_tsv_colnames <<- FALSE
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120 corcov_tsv_append <<- TRUE
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121 }
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122
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123 salience_tsv_colnames <- TRUE
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124 salience_tsv_append <- FALSE
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125 salience_tsv_action <- function(tsv) {
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126 tsv_action_factory(
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127 file = my_env$contrast_salience
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128 , colnames = salience_tsv_colnames
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129 , append = salience_tsv_append
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130 )(tsv)
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131 salience_tsv_colnames <<- FALSE
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132 salience_tsv_append <<- TRUE
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133 }
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134
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135 my_log( "-------------------------- Reading input data --------------------------")
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136
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137 # read_inputs is defined in w4mcorcov_input.R
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138 my_result <- read_inputs(input_env = my_env, failure_action = my_log)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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139
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140 if ( is.logical(my_result) && my_result) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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141 my_log( "-------------------------- Beginning data processing --------------------------")
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142
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143 # receiver for result of the call to corcov_calc
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144 my_result <- NULL
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145
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146 # compute and plot the correlation_vs_covariance details plot
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147 # The parameter settings here are generally taken from bioconductor ropls::plot.opls source.
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148 marVn <- c(4.6, 4.1, 2.6, 1.6)
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149 old_par <- par(
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150 font = 2 # bold font face
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151 , font.axis = 2 # bold font face for axis
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152 , font.lab = 2 # bold font face for x and y labels
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153 , lwd = 2 # line-width - interpretation is device spcific
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154 , mar = marVn # margins
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155 , pch = 18 # black diamond plot-character, see help for graphics::points
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156 # , mfrow = c(2,2) # two rows by two columns
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157 , pty = "s" # force plots to be square
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158 )
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159 plot2pdf(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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160 file.name = my_env$contrast_detail
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161 , width = 8
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162 , height = 8
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163 , plot.function = function() {
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164 # plot layout four plots per page
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165 layout(matrix(1:4, byrow = TRUE, nrow = 2))
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166 my_result <<- corcov_calc(
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167 calc_env = my_env
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168 , failure_action = my_fatal
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169 , progress_action = my_log
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170 , corcov_tsv_action = corcov_tsv_action
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171 , salience_tsv_action = salience_tsv_action
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172 )
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173 }
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174 )
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175 par(old_par)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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176
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177 my_log( "-------------------------- Finished data processing --------------------------")
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178 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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179
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180 my_log( "End of the '", modNamC, "' Galaxy module call")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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182 if (is.logical(my_result) && my_result) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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183 quit(save = "no", status = 0, runLast = TRUE)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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184 } else {
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185 my_log("failure :(")
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186 quit(save = "no", status = 10, runLast = TRUE)
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187 }