Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov_wrapper.R @ 0:50a07adddfbd draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
author eschen42
date Mon, 09 Oct 2017 15:46:13 -0400
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children e25fd8a13665
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50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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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
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66 # other parameters
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67
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68 my_env$tesC <- as.character(argVc["tesC"])
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69 my_env$facC <- as.character(argVc["facC"])
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70 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"])
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71 my_env$levCSV <- as.character(argVc["levCSV"])
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72 my_env$matchingC <- as.character(argVc["matchingC"])
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73 my_env$labelFeatures <- as.logical(argVc["labelFeatures"])
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74
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75 tsv_action_factory <- function(file, colnames, append) {
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76 return (
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77 function(tsv) {
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78 write.table(
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79 x = tsv
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80 , file = file
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81 , sep = "\t"
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82 , quote = FALSE
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83 , row.names = FALSE
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84 , col.names = colnames
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85 , append = append
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86 )
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87 }
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88 )
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89 }
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90
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91 corcov_tsv_colnames <- TRUE
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92 corcov_tsv_append <- FALSE
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93 corcov_tsv_action <- function(tsv) {
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94 tsv_action_factory(
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95 file = my_env$contrast_corcov
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96 , colnames = corcov_tsv_colnames
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97 , append = corcov_tsv_append
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98 )(tsv)
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99 corcov_tsv_colnames <<- FALSE
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100 corcov_tsv_append <<- TRUE
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101 }
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102
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103 my_log( "-------------------------- Reading input data --------------------------")
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104
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105 # read_inputs is defined in w4mcorcov_input.R
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106 my_result <- read_inputs(input_env = my_env, failure_action = my_log)
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107
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108 if ( is.logical(my_result) && my_result) {
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109 my_log( "-------------------------- Beginning data processing --------------------------")
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110
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111 # receiver for result of the call to corcov_calc
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112 my_result <- NULL
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113
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114 # compute and plot the correlation_vs_covariance details plot
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115 # The parameter settings here are generally taken from bioconductor ropls::plot.opls source.
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116 marVn <- c(4.6, 4.1, 2.6, 1.6)
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117 old_par <- par(
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118 font = 2 # bold font face
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119 , font.axis = 2 # bold font face for axis
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120 , font.lab = 2 # bold font face for x and y labels
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121 , lwd = 2 # line-width - interpretation is device spcific
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122 , mar = marVn # margins
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123 , pch = 18 # black diamond plot-character, see help for graphics::points
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124 # , mfrow = c(2,2) # two rows by two columns
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125 , pty = "s" # force plots to be square
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126 )
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127 plot2pdf(
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128 file.name = my_env$contrast_detail
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129 , width = 8
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130 , height = 8
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131 , plot.function = function() {
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132 # plot layout four plots per page
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133 layout(matrix(1:4, byrow = TRUE, nrow = 2))
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134 my_result <<- corcov_calc(
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135 calc_env = my_env
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136 , failure_action = my_fatal
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137 , progress_action = my_log
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138 , corcov_tsv_action = corcov_tsv_action
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139 )
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140 }
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141 )
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142 par(old_par)
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143
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144 my_log( "-------------------------- Finished data processing --------------------------")
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145 }
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146
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147 my_log( "End of the '", modNamC, "' Galaxy module call")
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148
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149 if (is.logical(my_result) && my_result) {
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150 quit(save = "no", status = 0, runLast = TRUE)
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151 } else {
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152 my_log("failure :(")
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153 quit(save = "no", status = 10, runLast = TRUE)
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154 }