Mercurial > repos > workflow4metabolomics > camera_groupcorr

annotate CAMERA_groupCorr.R @ 0:cb57be5de070 draft default tip

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planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
author workflow4metabolomics
date Sun, 24 Nov 2024 21:29:48 +0000
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1 #!/usr/bin/env Rscript
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2
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3 # ----- PACKAGE -----
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4 cat("\tSESSION INFO\n")
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5
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6 # Import the different functions
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7 source_local <- function(fname) {
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8 argv <- commandArgs(trailingOnly = FALSE)
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9 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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10 source(paste(base_dir, fname, sep = "/"))
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11 }
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12 source_local("lib.r")
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13
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14 pkgs <- c("CAMERA", "xcms", "multtest", "batch")
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15 loadAndDisplayPackages(pkgs)
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16 cat("\n\n")
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17 # ----- ARGUMENTS -----
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18 cat("\tARGUMENTS INFO\n")
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19
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20 args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
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21 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
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22
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23 cat("\n\n")
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24
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25 print("Arguments retrieved from the command line:")
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26 print(args)
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27
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28 # Function to convert "NULL" strings to actual NULL values
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29 convertNullString <- function(x) {
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30 if (x == "NULL") {
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31 return(NULL)
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32 }
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33 return(x)
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34 }
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35
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36 # Function to convert string to numeric lists
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37 convert_psg_list <- function(x) {
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38 # Check if x is NULL or has zero length before further processing
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39 if (is.null(x) || length(x) == 0) {
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40 return(NULL)
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41 }
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42
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43 # Force conversion to character
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44 x <- as.character(x)
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45
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46 if (grepl("^[0-9]+$", x)) {
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47 # If the string represents a single numeric value
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48 return(as.numeric(x))
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49 } else {
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50 # Convert string representation of a list to a numeric vector
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51 # Use a regular expression to split by common separators
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52 return(as.numeric(unlist(strsplit(x, "[,;\\s]+"))))
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53 }
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54 }
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55
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56 for (arg in names(args)) {
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57 args[[arg]] <- convertNullString(args[[arg]])
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58 }
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59
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60 # Convert only the 'psg_list' element in args
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61 args$psg_list <- convert_psg_list(args$psg_list)
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62
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63 print("Argument types:")
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64 print(sapply(args, class))
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65
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66 # Check if the image file exists
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67 if (!file.exists(args$image)) {
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68 stop("The RData file does not exist: ", args$image)
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69 }
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70
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71 # ----- PROCESSING INFILE -----
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72
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73 # Load the RData file
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74 load(args$image)
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75 args$image <- NULL
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76
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77 # Save arguments to generate a report
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78 if (!exists("listOFlistArguments")) listOFlistArguments <- list()
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79 listOFlistArguments[[format(Sys.time(), "%y%m%d-%H:%M:%S_groupCorr")]] <- args
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80
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81 # We unzip automatically the chromatograms from the zip files.
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82 if (!exists("zipfile")) zipfile <- NULL
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83 if (!exists("singlefile")) singlefile <- NULL
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84 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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85 zipfile <- rawFilePath$zipfile
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86 singlefile <- rawFilePath$singlefile
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87 args <- rawFilePath$args
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88
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89 print(paste("singlefile :", singlefile))
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90 if (!is.null(singlefile)) {
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91 directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
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92 }
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93
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94 # Ensure the xa object is loaded
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95 if (!exists("xa")) {
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96 stop("The xa object was not found in the RData file.")
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97 }
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98
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99 print("xa object loaded:")
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100 print(xa)
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101
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102 # Apply the groupCorr function to the xsAnnotate object
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103 print("Calling groupCorr function:")
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104 xa <- groupCorr(xa, cor_eic_th = args$cor_eic_th, pval = args$pval, graphMethod = args$graphMethod, calcIso = args$calcIso, calcCiS = args$calcCiS, calcCaS = args$calcCaS, psg_list = args$psg_list, cor_exp_th = args$cor_exp_th, intval = args$intval)
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105
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106 print("Result of groupCorr function:")
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107 print(xa)
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108
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109 # Extract the list of annotated peaks
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110 peakList <- getPeaklist(xa, intval = args$intval)
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111
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112 if (length(phenoData@data$sample_name) == 1) {
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113 peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
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114 variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
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115 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
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116 } else {
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117 names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
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118 names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals
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119
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120 variableMetadata <- data.frame(
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121 name = names_default,
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122 name_custom = names_custom,
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123 stringsAsFactors = FALSE
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124 )
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125 variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
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126 }
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127
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128 if (!exists("RTinMinute")) RTinMinute <- FALSE
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129
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130 if (args$convertRTMinute == TRUE && RTinMinute == FALSE) {
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131 RTinMinute <- TRUE
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132 variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
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133 }
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134
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135 # Save the extracted peak list as a TSV file named 'variableMetadata.tsv'
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136 output_file_tsv <- "variableMetadata.tsv"
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137 write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FALSE, quote = FALSE)
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138
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139 # Save the updated xsAnnotate object
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140 output_file_RData <- "camera_groupCorr.RData"
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141 objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData")
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142 save(list = objects2save[objects2save %in% ls()], file = output_file_RData)
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143
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144 cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")