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annotate checkformat_script.R @ 1:b642f4f87022 draft

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
author ethevenot
date Thu, 11 Jan 2018 10:26:11 -0500
parents 059eb452931e
children 7d59cbf49966
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059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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diff changeset
1 ## Etienne Thevenot
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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2 ## CEA, MetaboHUB Paris
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3 ## etienne.thevenot@cea.fr
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7 ## Reads the dataMatrix, sampleMetadata, and variableMetadata .tsv files
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8 ## and checks the formats
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9 readAndCheckF <- function(datFilC="dataMatrix.tsv",
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10 samFilC="sampleMetadata.tsv",
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11 varFilC="variableMetadata.tsv",
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12 makNamL) {
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15 ## options
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17 optStrAsFacL <- options()[["stringsAsFactors"]]
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18 options(stringsAsFactors = FALSE)
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21 ## checking that the tables have no duplicated row or column names
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23 for(tabC in c("dat", "sam", "var")) {
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25 tabNamC <- switch(tabC, dat="dataMatrix", sam="sampleMetadata", var="variableMetadata")
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27 rowVc <- read.table(eval(parse(text=paste0(tabC, "FilC"))),
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28 check.names = FALSE,
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29 header = TRUE,
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30 sep = "\t")[, 1]
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32 colVc <- unlist(read.table(eval(parse(text=paste0(tabC, "FilC"))),
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33 check.names = FALSE,
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34 nrow=1,
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35 sep = "\t"))[-1]
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37 if(any(duplicated(rowVc)))
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38 stop("The following row name(s) is/are duplicated in the ",
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39 tabNamC,
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40 " table: '",
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41 paste(rowVc[duplicated(rowVc)], collapse="', '"), "'",
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42 call.=FALSE)
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44 if(any(duplicated(colVc)))
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45 stop("The following column name(s) is/are duplicated in the ",
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46 tabNamC,
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47 " table: '",
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48 paste(colVc[duplicated(colVc)], collapse="', '"), "'",
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49 call.=FALSE)
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51 }
1
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0
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53
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54 ## reading tables
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55
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56 datMN <- t(as.matrix(read.table(datFilC,
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57 check.names = FALSE,
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58 header = TRUE,
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59 row.names = 1,
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60 sep = "\t")))
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61
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62 samDF <- read.table(samFilC,
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63 check.names = FALSE,
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64 header = TRUE,
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65 row.names = 1,
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66 sep = "\t")
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67
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68 varDF <- read.table(varFilC,
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69 check.names = FALSE,
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70 header = TRUE,
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71 row.names = 1,
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72 sep = "\t")
1
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0
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74
1
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75 ## checking that dataMatrix is numeric and that the sample and variable numbers are coherent
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76
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77 if(mode(datMN) != "numeric") {
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78 stop("The dataMatrix is not of the 'numeric' type",
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79 call. = FALSE)
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80 }
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81
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82 if(nrow(datMN) != nrow(samDF)) {
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83 if(nrow(datMN) > nrow(samDF)) {
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84 print(setdiff(rownames(datMN), rownames(samDF)))
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85 stop("The sample names above from dataMatrix were not found in sampleMetadata")
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86 } else {
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87 print(setdiff(rownames(samDF), rownames(datMN)))
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88 stop("The sample names above from sampleMetadata were not found in dataMatrix")
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89 }
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90 }
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91
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92 if(ncol(datMN) != nrow(varDF)) {
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93 if(ncol(datMN) > nrow(varDF)) {
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94 print(setdiff(colnames(datMN), rownames(varDF)))
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95 stop("The variable names above from dataMatrix were not found in variableMetadata")
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96 } else {
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97 print(setdiff(rownames(varDF), colnames(datMN)))
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98 stop("The variable names above from variableMetadata were not found in dataMatrix")
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99 }
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100 }
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101
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102
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103 ## making sample and variable names (optional)
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104
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105 newL <- FALSE
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106
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107 if(makNamL) {
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108
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109 cat("\n\nMessage: Converting sample and variable names to the standard R format\n")
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110
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111 rownames(datMN) <- make.names(rownames(datMN), unique = TRUE)
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112 colnames(datMN) <- make.names(colnames(datMN), unique = TRUE)
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113 rownames(samDF) <- make.names(rownames(samDF), unique = TRUE)
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114 rownames(varDF) <- make.names(rownames(varDF), unique = TRUE)
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115
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116 newL <- TRUE
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117
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118 }
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119
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120
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121 ## checking sample and variable names
0
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122
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123 chkL <- TRUE
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124
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125 if(!identical(rownames(datMN), rownames(samDF))) {
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126
1
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127 if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) {
0
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128
1
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129 cat("\n\nMessage: Re-ordering dataMatrix sample names to match sampleMetadata\n")
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130 datMN <- datMN[rownames(samDF), , drop = FALSE]
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131
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132 stopifnot(identical(sort(rownames(datMN)), sort(rownames(samDF))))
0
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133
1
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134 newL <- TRUE
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135
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136 } else {
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137
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138 cat("\n\nStop: The sample names of dataMatrix and sampleMetadata do not match:\n")
0
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139 print(cbind.data.frame(indice = 1:nrow(datMN),
1
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140 dataMatrix=rownames(datMN),
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141 sampleMetadata=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
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142 chkL <- FALSE
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143
0
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144 }
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145
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146 }
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147
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148 if(!identical(colnames(datMN), rownames(varDF))) {
1
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149
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150 if(identical(sort(colnames(datMN)), sort(rownames(varDF)))) {
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151
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152 cat("\n\nMessage: Re-ordering dataMatrix variable names to match variableMetadata\n")
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153 datMN <- datMN[, rownames(varDF), drop = FALSE]
0
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154
1
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155 stopifnot(identical(sort(colnames(datMN)), sort(rownames(varDF))))
0
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156
1
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157 newL <- TRUE
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158
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159 } else {
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160
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161 cat("\n\nStop: The variable names of dataMatrix and variableMetadata do not match:\n")
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162 print(cbind.data.frame(indice = 1:ncol(datMN),
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163 dataMatrix=colnames(datMN),
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164 variableMetadata=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE])
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165 chkL <- FALSE
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166
0
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167 }
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168
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169 }
1
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170
0
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171
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172 options(stringsAsFactors=optStrAsFacL)
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173
1
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174 resLs <- list(chkL=chkL,
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175 newL = newL,
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176 datMN = datMN,
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177 samDF = samDF,
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178 varDF = varDF)
0
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179
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180 return(resLs)
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181
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182 } ## end of checkAndReadF
1
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183
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184
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185
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186
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187 ## if(!identical(rownames(datMN), rownames(samDF))) {
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188 ## ## checking sample names
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189
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190 ## chkL <- FALSE
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191
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192 ## datSamDifVc <- setdiff(rownames(datMN), rownames(samDF))
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193
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194 ## if(length(datSamDifVc)) {
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195 ## cat("\nThe following samples were found in the dataMatrix column names but not in the sampleMetadata row names:\n", sep="")
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196 ## print(cbind.data.frame(col = as.numeric(sapply(datSamDifVc, function(samC) which(rownames(datMN) == samC))),
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197 ## name = datSamDifVc))
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198 ## }
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199
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200 ## samDatDifVc <- setdiff(rownames(samDF), rownames(datMN))
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201
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202 ## if(length(samDatDifVc)) {
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203 ## cat("\n\nThe following samples were found in the sampleMetadata row names but not in the dataMatrix column names:\n", sep="")
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204 ## print(cbind.data.frame(row = as.numeric(sapply(samDatDifVc, function(samC) which(rownames(samDF) == samC))),
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205 ## name = samDatDifVc))
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206 ## }
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207
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208 ## if(nrow(datMN) != nrow(samDF)) {
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209 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " columns (ie samples) whereas the sampleMetadata has ", nrow(samDF), " rows\n", sep="")
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210 ## } else if(identical(gsub("^X", "", rownames(datMN)), rownames(samDF))) {
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211 ## cat("\n\nThe dataMatrix column names start with an 'X' but not the sampleMetadata row names\n", sep="")
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212 ## } else if(identical(gsub("^X", "", rownames(samDF)), rownames(datMN))) {
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213 ## cat("\n\nThe sampleMetadata row names start with an 'X' but not the dataMatrix column names\n", sep="")
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214 ## } else if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) {
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215 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not in the same order:\n", sep="")
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216 ## print(cbind.data.frame(indice = 1:nrow(datMN),
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217 ## dataMatrix_columnnames=rownames(datMN),
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218 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
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219 ## } else {
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220 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not identical:\n", sep="")
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221 ## print(cbind.data.frame(indice = 1:nrow(datMN),
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222 ## dataMatrix_columnnames=rownames(datMN),
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223 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
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224 ## }
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225
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226 ## }
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227 ## datRowVc <- rownames(datMN)
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228 ## datRowMakVc <- make.names(datRowVc, unique = TRUE)
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229 ## if(datRowMakVc != datRowVc) {
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230 ## rownames(datMN) <- datRowMakVc
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231 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format\n")
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232 ## }
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233
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234 ## datColVc <- colnames(datMN)
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235 ## datColMakVc <- make.names(datColVc, unique = TRUE)
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236 ## if(datColMakVc != datColVc) {
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237 ## colnames(datMN) <- datColMakVc
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238 ## cat("\n\nMessage: The variable names of the dataMatrix have been converted to the standard R format\n")
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239 ## }
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240
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241 ## samRowVc <- rownames(datMN)
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242 ## samRowMakVc <- make.names(samRowVc, unique = TRUE)
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243 ## if(samRowMakVc != samRowVc) {
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244 ## rownames(datMN) <- samRowMakVc
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245 ## cat("\n\nMessage: The sample names of the sampleMetadata have been converted to the standard R format\n")
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246 ## }
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247
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248 ## datRowVc <- rownames(datMN)
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249 ## datRowMakVc <- make.names(datRowVc, unique = TRUE)
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250 ## if(datRowMakVc != datRowVc) {
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251 ## rownames(datMN) <- datRowMakVc
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252 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format\n")
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253 ## }
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254
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255 ## }
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256
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257 ## checking names (optional)
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258
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259
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260
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261
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262 ## datRowMakVc <- make.names(datRowVc, unique = TRUE)
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263 ## if(datRowMakVc != datRowVc) {
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264 ## if(makNamL) {
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265 ## rownames(datMN) <- datRowMakVc
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266 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format; select the make names argument to convert them\n")
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267 ## } else {
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268 ## cat("\n\nWarning: Some of the sample names of the dataMatrix are not in the standard R format; select the make names argument to convert them\n")
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269 ## }
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270
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271 ## if(makNamL) {
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272
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273 ## rownames(datMN) <- make.names(rownames(datMN), unique = TRUE)
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274 ## colnames(datMN) <- make.names(colnames(datMN), unique = TRUE)
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275 ## rownames(samDF) <- make.names(rownames(samDF), unique = TRUE)
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276 ## rownames(varDF) <- make.names(rownames(varDF), unique = TRUE)
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277
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278 ## }
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279 ## checking sample names
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280
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281 ## if(nrow(datMN) == nrow(samDF)) {
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282
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283
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284
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285 ## }
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286
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287 ## chkL <- FALSE
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288
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289 ## datSamDifVc <- setdiff(rownames(datMN), rownames(samDF))
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290
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291 ## if(length(datSamDifVc)) {
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292 ## cat("\nThe following samples were found in the dataMatrix column names but not in the sampleMetadata row names:\n", sep="")
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293 ## print(cbind.data.frame(col = as.numeric(sapply(datSamDifVc, function(samC) which(rownames(datMN) == samC))),
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294 ## name = datSamDifVc))
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295 ## }
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296
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297 ## samDatDifVc <- setdiff(rownames(samDF), rownames(datMN))
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298
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299 ## if(length(samDatDifVc)) {
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300 ## cat("\n\nThe following samples were found in the sampleMetadata row names but not in the dataMatrix column names:\n", sep="")
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301 ## print(cbind.data.frame(row = as.numeric(sapply(samDatDifVc, function(samC) which(rownames(samDF) == samC))),
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302 ## name = samDatDifVc))
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303 ## }
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304
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305 ## if(nrow(datMN) != nrow(samDF)) {
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306 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " columns (ie samples) whereas the sampleMetadata has ", nrow(samDF), " rows\n", sep="")
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307 ## } else if(identical(gsub("^X", "", rownames(datMN)), rownames(samDF))) {
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308 ## cat("\n\nThe dataMatrix column names start with an 'X' but not the sampleMetadata row names\n", sep="")
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309 ## } else if(identical(gsub("^X", "", rownames(samDF)), rownames(datMN))) {
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310 ## cat("\n\nThe sampleMetadata row names start with an 'X' but not the dataMatrix column names\n", sep="")
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311 ## } else if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) {
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312 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not in the same order:\n", sep="")
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313 ## print(cbind.data.frame(indice = 1:nrow(datMN),
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314 ## dataMatrix_columnnames=rownames(datMN),
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315 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
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316 ## } else {
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317 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not identical:\n", sep="")
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318 ## print(cbind.data.frame(indice = 1:nrow(datMN),
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319 ## dataMatrix_columnnames=rownames(datMN),
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320 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
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321 ## }
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322
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323 ## }
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324
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325
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326 ## if(!identical(colnames(datMN), rownames(varDF))) {
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327 ## ## checking variable names
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328
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329 ## chkL <- FALSE
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330
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331 ## datVarDifVc <- setdiff(colnames(datMN), rownames(varDF))
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332
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333 ## if(length(datVarDifVc)) {
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334 ## cat("\nThe following variables were found in the dataMatrix row names but not in the variableMetadata row names:\n", sep="")
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335 ## print(cbind.data.frame(row = as.numeric(sapply(datVarDifVc, function(varC) which(colnames(datMN) == varC))),
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336 ## name = datVarDifVc))
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337
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338 ## }
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339
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340 ## varDatDifVc <- setdiff(rownames(varDF), colnames(datMN))
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341
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342 ## if(length(varDatDifVc)) {
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343 ## cat("\n\nThe following variables were found in the variableMetadata row names but not in the dataMatrix row names:\n", sep="")
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344 ## print(cbind.data.frame(row = as.numeric(sapply(varDatDifVc, function(varC) which(rownames(varDF) == varC))),
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345 ## name = varDatDifVc))
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346 ## }
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347
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348 ## if(ncol(datMN) != nrow(varDF)) {
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349 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " rows (ie variables) whereas the variableMetadata has ", nrow(varDF), " rows\n", sep="")
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350 ## } else if(identical(sort(colnames(datMN)), sort(rownames(varDF)))) {
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351 ## cat("\n\nThe dataMatrix row names and the variableMetadata row names are not in the same order:\n", sep="")
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352 ## print(cbind.data.frame(row = 1:ncol(datMN),
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353 ## dataMatrix_rownames=colnames(datMN),
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354 ## variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE])
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355 ## } else {
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356 ## cat("\n\nThe dataMatrix row names and the variableMetadata row names are not identical:\n", sep="")
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357 ## print(cbind.data.frame(row = 1:ncol(datMN),
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358 ## dataMatrix_rownames=colnames(datMN),
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359 ## variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE])
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360 ## }
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361 ## }
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362 ## checkF <- function(datInpMN,
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363 ## samInpDF,
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364 ## varInpDF) {
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365
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366 ## mode(datInpMN) == "numeric" &&
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367 ## identical(rownames(datInpMN), rownames(samInpDF)) &&
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368 ## identical(colnames(datInpMN), rownames(varInpDF))
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369
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370
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371 ## }