Mercurial > repos > recetox > waveica

annotate waveica_wrapper.R @ 6:cf3f2f964d80 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
author recetox
date Thu, 29 Sep 2022 15:20:18 +0000
parents 8b55efc7d117
children 385b1221be44
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cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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1 read_file <- function(file, metadata, ft_ext, mt_ext) {
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2 data <- read_data(file, ft_ext)
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4 if (!is.na(metadata)) {
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5 mt_data <- read_data(metadata, mt_ext)
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6 data <- merge(mt_data, data, by = "sampleName")
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7 }
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8
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9 return(data)
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10 }
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12 read_data <- function(file, ext) {
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13 if (ext == "csv") {
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14 data <- read.csv(file, header = TRUE)
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15 } else if (ext == "tsv") {
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16 data <- read.csv(file, header = TRUE, sep = "\t")
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17 } else {
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18 data <- arrow::read_parquet(file)
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19 }
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21 return(data)
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22 }
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24 waveica <- function(file,
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25 metadata = NA,
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26 ext,
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27 wavelet_filter,
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28 wavelet_length,
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29 k,
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30 t,
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31 t2,
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32 alpha,
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33 exclude_blanks) {
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34
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35 # get input from the Galaxy, preprocess data
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36 ext <- strsplit(x = ext, split = "\\,")[[1]]
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38 ft_ext <- ext[1]
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39 mt_ext <- ext[2]
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41 data <- read_file(file, metadata, ft_ext, mt_ext)
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42
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43 required_columns <- c("sampleName", "class", "sampleType", "injectionOrder", "batch")
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44 verify_input_dataframe(data, required_columns)
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46 data <- sort_by_injection_order(data)
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47
2
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48 # separate data into features, batch and group
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49 feature_columns <- colnames(data)[!colnames(data) %in% required_columns]
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50 features <- data[, feature_columns]
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51 group <- enumerate_groups(as.character(data$sampleType))
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52 batch <- data$batch
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54 # run WaveICA
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55 features <- recetox.waveica::waveica(
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56 data = features,
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57 wf = get_wf(wavelet_filter, wavelet_length),
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58 batch = batch,
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59 group = group,
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60 K = k,
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61 t = t,
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62 t2 = t2,
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63 alpha = alpha
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64 )
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66 data[, feature_columns] <- features
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68 # remove blanks from dataset
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69 if (exclude_blanks) {
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70 data <- exclude_group(data, group)
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71 }
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73 return(data)
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74 }
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76 waveica_singlebatch <- function(file,
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77 metadata = NA,
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78 ext,
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79 wavelet_filter,
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80 wavelet_length,
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81 k,
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82 alpha,
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83 cutoff,
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84 exclude_blanks) {
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85
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86 # get input from the Galaxy, preprocess data
6
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87 ext <- strsplit(x = ext, split = "\\,")[[1]]
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88
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89 ft_ext <- ext[1]
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90 mt_ext <- ext[2]
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91
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92 data <- read_file(file, metadata, ft_ext, mt_ext)
4
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93
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94 required_columns <- c("sampleName", "class", "sampleType", "injectionOrder")
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95 optional_columns <- c("batch")
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96 verify_input_dataframe(data, required_columns)
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97
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98 data <- sort_by_injection_order(data)
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99
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100 feature_columns <- colnames(data)[!colnames(data) %in% c(required_columns, optional_columns)]
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101 features <- data[, feature_columns]
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102 injection_order <- data$injectionOrder
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103
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104 # run WaveICA
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105 features <- recetox.waveica::waveica_nonbatchwise(
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106 data = features,
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107 wf = get_wf(wavelet_filter, wavelet_length),
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108 injection_order = injection_order,
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109 K = k,
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110 alpha = alpha,
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111 cutoff = cutoff
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112 )
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113
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114 data[, feature_columns] <- features
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115
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116 # remove blanks from dataset
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117 if (exclude_blanks) {
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118 data <- exclude_group(data, group)
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119 }
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120
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121 return(data)
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122 }
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123
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124
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125 sort_by_injection_order <- function(data) {
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126 if ("batch" %in% colnames(data)) {
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127 data <- data[order(data[, "batch"],
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128 data[, "injectionOrder"],
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129 decreasing = FALSE
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130 ), ]
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131 } else {
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132 data <- data[order(data[, "injectionOrder"],
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133 decreasing = FALSE
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134 ), ]
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135 }
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136 return(data)
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137 }
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138
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139
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140 verify_input_dataframe <- function(data, required_columns) {
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141 if (anyNA(data)) {
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142 stop("Error: dataframe cannot contain NULL values!
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143 Make sure that your dataframe does not contain empty cells")
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144 } else if (!all(required_columns %in% colnames(data))) {
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145 stop("Error: missing metadata!
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146 Make sure that the following columns are present in your dataframe: ", paste(required_columns, collapse = ", "))
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147 }
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148 }
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149
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150
1
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151 # Match group labels with [blank/sample/qc] and enumerate them
2
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152 enumerate_groups <- function(group) {
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153 group[grepl("blank", tolower(group))] <- 0
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154 group[grepl("sample", tolower(group))] <- 1
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155 group[grepl("qc", tolower(group))] <- 2
0
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156
2
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157 return(group)
0
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158 }
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159
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160
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161 # Create appropriate input for R wavelets function
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162 get_wf <- function(wavelet_filter, wavelet_length) {
2
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163 wf <- paste(wavelet_filter, wavelet_length, sep = "")
0
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164
2
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165 # exception to the wavelet function
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166 if (wf == "d2") {
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167 wf <- "haar"
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168 }
0
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169
2
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170 return(wf)
0
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171 }
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172
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173
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174 # Exclude blanks from a dataframe
2
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175 exclude_group <- function(data, group) {
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176 row_idx_to_exclude <- which(group %in% 0)
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177 if (length(row_idx_to_exclude) > 0) {
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178 data_without_blanks <- data[-c(row_idx_to_exclude), ]
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179 cat("Blank samples have been excluded from the dataframe.\n")
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180 return(data_without_blanks)
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181 } else {
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182 return(data)
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183 }
0
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184 }
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185
6
cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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186 store_data <- function(data, output, ext) {
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187 if (ext == "csv") {
cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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188 write.csv(data, file = output, row.names = FALSE, quote = FALSE)
cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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189 } else if (ext == "tsv") {
cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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190 write.table(data, file = output, sep = "\t", row.names = FALSE, quote = FALSE)
cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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191 } else {
cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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192 arrow::write_parquet(data, sink = output)
cf3f2f964d80 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit d82e7dad96bebe9424ac7bf490e2786d82c3681a
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193 }
2
d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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194 cat("Normalization has been completed.\n")
0
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195 }