Mercurial > repos > workflow4metabolomics > mixmodel4repeated_measures

annotate mixmodel_wrapper.R @ 0:a4d89d47646f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
author workflow4metabolomics
date Mon, 16 May 2022 09:25:01 +0000
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a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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1 #!/usr/bin/env Rscript
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3 library(lme4) ## mixed model computing
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4 library(Matrix)
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5 library(MASS)
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6 library(lmerTest) ## computing pvalue and lsmeans from results of lme4 package
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7 library(multtest) ## multiple testing
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8 library(ggplot2)
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9 library(gridExtra)
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10 library(grid)
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12 source_local <- function(fname) {
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13 argv <- commandArgs(trailingOnly = FALSE)
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14 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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15 source(paste(base_dir, fname, sep = "/"))
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16 }
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18 source_local("mixmodel_script.R")
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19 source_local("diagmfl.R")
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21 parse_args <- function() {
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22 args <- commandArgs()
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23 start <- which(args == "--args")[1] + 1
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24 if (is.na(start)) {
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25 return(list())
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26 }
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27 seq_by2 <- seq(start, length(args), by = 2)
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28 result <- as.list(args[seq_by2 + 1])
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29 names(result) <- args[seq_by2]
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30 return(result)
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31 }
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33 argVc <- unlist(parse_args())
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35 ##------------------------------
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36 ## Initializing
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37 ##------------------------------
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39 ## options
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40 ##--------
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42 strAsFacL <- options()$stringsAsFactors
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43 options(stringsAsFactors = FALSE)
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45 ## constants
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46 ##----------
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48 modNamC <- "mixmodel" ## module name
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50 topEnvC <- environment()
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51 flagC <- "\n"
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53 ## functions
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54 ##----------
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56 flgF <- function(tesC,
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57 envC = topEnvC,
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58 txtC = NA) { ## management of warning and error messages
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59
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60 tesL <- eval(parse(text = tesC), envir = envC)
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62 if (!tesL) {
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64 sink(NULL)
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65 stpTxtC <- ifelse(is.na(txtC),
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66 paste0(tesC, " is FALSE"),
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67 txtC)
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68
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69 stop(stpTxtC,
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70 call. = FALSE)
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72 }
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74 } ## flgF
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75
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76 ## log file
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77 ##---------
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79 sink(argVc["information"])
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80
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81 cat("\nStart of the '", modNamC, "' Galaxy module call: ", format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
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82 cat("\nParameters used:\n\n")
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83 print(argVc)
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84 cat("\n\n")
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85
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86 ## loading
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87 ##--------
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88
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89 datMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
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90 check.names = FALSE,
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91 header = TRUE,
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92 row.names = 1,
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93 sep = "\t")))
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94
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95 samDF <- read.table(argVc["sampleMetadata_in"],
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96 check.names = FALSE,
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97 header = TRUE,
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98 row.names = 1,
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99 sep = "\t")
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100
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101 varDF <- read.table(argVc["variableMetadata_in"],
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102 check.names = FALSE,
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103 header = TRUE,
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104 row.names = 1,
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105 sep = "\t")
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106
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107
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108 ## checking
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109 ##---------
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110
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111 flgF("identical(rownames(datMN), rownames(samDF))", txtC = "Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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112 flgF("identical(colnames(datMN), rownames(varDF))", txtC = "Row names of the dataMatrix are not identical to the row names of the variableMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
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113
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114 flgF("argVc['time'] %in% colnames(samDF)", txtC = paste0("Required time factor '", argVc["time"], "' could not be found in the column names of the sampleMetadata"))
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115 flgF("argVc['subject'] %in% colnames(samDF)", txtC = paste0("Required subject factor '", argVc["subject"], "' could not be found in the column names of the sampleMetadata"))
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116
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117 flgF("mode(samDF[, argVc['time']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc["time"], "' column of the sampleMetadata should contain either number only, or character only"))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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118 flgF("mode(samDF[, argVc['subject']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc["subject"], "' column of the sampleMetadata should contain either number only, or character only"))
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119
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120 flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')")
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121 flgF("argVc['trf'] %in% c('none', 'log10', 'log2')")
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122
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123 flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1", txtC = "(corrected) p-value threshold must be between 0 and 1")
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124 flgF("argVc['diaR'] %in% c('no', 'yes')")
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125
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126
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127 ##------------------------------
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128 ## Formating
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129 ##------------------------------
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130
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131 if (argVc["dff"] == "Satt") {
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132 dffmeth <- "Satterthwaite"
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133 } else {
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134 dffmeth <- "Kenward-Roger"
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135 }
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136
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137
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138 ##------------------------------
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139 ## Computation
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140 ##------------------------------
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141
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142
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143 varDFout <- lmixedm(datMN = datMN,
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144 samDF = samDF,
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145 varDF = varDF,
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146 fixfact = argVc["fixfact"],
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147 time = argVc["time"],
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148 subject = argVc["subject"],
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149 logtr = argVc["trf"],
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150 pvalCutof = argVc["thrN"],
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151 pvalcorMeth = argVc["adjC"],
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152 dffOption = dffmeth,
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153 visu = argVc["diaR"],
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154 least.confounded = FALSE,
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155 outlier.limit = 3,
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156 pdfC = argVc["out_graph_pdf"],
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157 pdfE = argVc["out_estim_pdf"]
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158 )
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159
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160
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161
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162
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163 ##------------------------------
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164 ## Rounding
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165 ##------------------------------
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166
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167 if (argVc["rounding"] == "yes") {
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168 varDFout[, which(!(colnames(varDFout) %in% colnames(varDF)))] <- apply(varDFout[, which(!(colnames(varDFout) %in% colnames(varDF)))], 2, round, digits = as.numeric(argVc["decplaces"]))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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169 }
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170
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171 ##------------------------------
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172 ## Ending
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173 ##------------------------------
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174
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175
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176 ## saving
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177 ##--------
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178
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179 varDFout <- cbind.data.frame(variableMetadata = rownames(varDFout),
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180 varDFout)
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181
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182 write.table(varDFout,
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183 file = argVc["variableMetadata_out"],
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184 quote = FALSE,
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185 row.names = FALSE,
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186 sep = "\t")
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187
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188 ## closing
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189 ##--------
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190
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191 cat("\n\nEnd of '", modNamC, "' Galaxy module call: ",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
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192 as.character(Sys.time()), "\n", sep = "")
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193 cat("\nInformation about R (version, Operating System, attached or loaded packages):\n\n")
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194 sessionInfo()
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195
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196 sink()
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197
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198 options(stringsAsFactors = strAsFacL)
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199
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200 rm(list = ls())