Mercurial > repos > ethevenot > univariate

annotate tests/univariate_tests.R @ 0:ef64d3752050 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
author ethevenot
date Wed, 27 Jul 2016 11:44:34 -0400
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ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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1 library(RUnit)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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3 wrapperF <- function(argVc) {
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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6 source("../univariate_script.R")
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9 #### Start_of_testing_code <- function() {}
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12 ##------------------------------
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13 ## Initializing
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14 ##------------------------------
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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 ## packages
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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23 ##---------
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25 library(PMCMR)
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27 ## constants
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28 ##----------
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30 modNamC <- "Univariate" ## module name
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32 topEnvC <- environment()
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33 flagC <- "\n"
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35 ## functions
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36 ##----------
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38 flgF <- function(tesC,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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39 envC = topEnvC,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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40 txtC = NA) { ## management of warning and error messages
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42 tesL <- eval(parse(text = tesC), envir = envC)
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44 if(!tesL) {
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46 sink(NULL)
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47 stpTxtC <- ifelse(is.na(txtC),
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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48 paste0(tesC, " is FALSE"),
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49 txtC)
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51 stop(stpTxtC,
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52 call. = FALSE)
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54 }
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56 } ## flgF
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58 ## log file
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59 ##---------
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61 sink(argVc["information"])
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62
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63 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
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64 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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65
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66 ## loading
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67 ##--------
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68
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69 datMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
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70 check.names = FALSE,
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71 header = TRUE,
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72 row.names = 1,
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73 sep = "\t")))
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75 samDF <- read.table(argVc["sampleMetadata_in"],
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76 check.names = FALSE,
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77 header = TRUE,
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78 row.names = 1,
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79 sep = "\t")
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81 varDF <- read.table(argVc["variableMetadata_in"],
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82 check.names = FALSE,
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83 header = TRUE,
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84 row.names = 1,
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85 sep = "\t")
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86
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87 tesC <- argVc["tesC"]
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88
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89 ## checking
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90 ##---------
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91
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92 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")
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93 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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95 flgF("argVc['facC'] %in% colnames(samDF)", txtC = paste0("Required factor of interest '", argVc['facC'], "' could not be found in the column names of the sampleMetadata"))
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96 flgF("mode(samDF[, argVc['facC']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc['facC'], "' column of the sampleMetadata should contain either number only, or character only"))
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98 flgF("!(tesC %in% c('ttest', 'wilcoxon')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) == 2)", txtC = paste0("For 'ttest' and 'wilcoxon', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with only two different classes"))
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99 flgF("!(tesC %in% c('anova', 'kruskal')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) > 2)", txtC = paste0("For 'anova' and 'kruskal', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with at least three different classes"))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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100 flgF("!(tesC %in% c('pearson', 'spearman')) || mode(samDF[, argVc['facC']]) == 'numeric'", txtC = paste0("For 'pearson' and 'spearman', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain numbers only"))
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101
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102 flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')")
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103
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104 flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1",
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105 txtC = "(corrected) p-value threshold must be between 0 and 1")
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106
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107
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108 ##------------------------------
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109 ## Computation
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110 ##------------------------------
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111
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112
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113 varDF <- univariateF(datMN = datMN,
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114 samDF = samDF,
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115 varDF = varDF,
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116 facC = argVc["facC"],
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117 tesC = tesC,
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118 adjC = argVc["adjC"],
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119 thrN = as.numeric(argVc["thrN"]))
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120
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121
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122 ##------------------------------
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123 ## Ending
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124 ##------------------------------
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125
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126
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127 ## saving
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128 ##--------
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129
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130 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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131 varDF)
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132 write.table(varDF,
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133 file = argVc["variableMetadata_out"],
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134 quote = FALSE,
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135 row.names = FALSE,
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136 sep = "\t")
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137
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138 ## closing
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139 ##--------
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140
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141 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
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142 as.character(Sys.time()), "\n", sep = "")
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143
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144 sink()
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145
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146 options(stringsAsFactors = strAsFacL)
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147
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148
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149
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150 #### End_of_testing_code <- function() {}
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151
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152
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153 return(list(varDF = varDF))
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154
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155 rm(list = ls())
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156
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parents:
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157 }
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158
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159 exaDirOutC <- "output"
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160 if(!file.exists(exaDirOutC))
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161 stop("Please create an 'output' subfolder into the (current) 'tests' folder")
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162
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163 tesArgLs <- list(input_kruskal = c(facC = "ageGroup",
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164 tesC = "kruskal",
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165 adjC = "fdr",
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166 thrN = "0.05",
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167 .chkC = "checkEqualsNumeric(outLs[['varDF']]['HMDB01032', 'ageGroup_kruskal_senior-experienced_pva'], 0.1231246, tolerance = 1e-6)"),
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168 example1_wilcoxDif = c(facC = "jour",
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169 tesC = "wilcoxon",
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170 adjC = "fdr",
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171 thrN = "0.05",
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172 .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_wilcoxon_J3-J10_dif'], 0.216480042, tolerance = 1e-8)"),
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173 example1_ttestFdr = c(facC = "jour",
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174 tesC = "ttest",
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175 adjC = "fdr",
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176 thrN = "0.05",
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177 .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_ttest_J3-J10_fdr'], 0.7605966, tolerance = 1e-6)"))
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178
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179 for(tesC in names(tesArgLs))
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180 tesArgLs[[tesC]] <- c(tesArgLs[[tesC]],
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parents:
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181 dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"),
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182 sampleMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "sampleMetadata.tsv"),
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parents:
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183 variableMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "variableMetadata.tsv"),
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parents:
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184 variableMetadata_out = file.path(exaDirOutC, "variableMetadata.tsv"),
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185 information = file.path(exaDirOutC, "information.txt"))
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186
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parents:
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187 for(tesC in names(tesArgLs)) {
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parents:
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188 print(tesC)
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parents:
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189 outLs <- wrapperF(tesArgLs[[tesC]])
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parents:
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190 if(".chkC" %in% names(tesArgLs[[tesC]]))
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parents:
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191 stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]])))
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192 }
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193
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194 message("Checks successfully completed")