--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib.r	Sun Nov 24 21:28:57 2024 +0000
@@ -0,0 +1,391 @@
+# lib.r
+
+# @author G. Le Corguille
+# solve an issue with batch if arguments are logical TRUE/FALSE
+parseCommandArgs <- function(...) {
+  args <- batch::parseCommandArgs(...)
+  for (key in names(args)) {
+    if (args[key] %in% c("TRUE", "FALSE")) {
+      args[key] <- as.logical(args[key])
+    }
+  }
+  return(args)
+}
+
+# @author G. Le Corguille
+# This function will
+# - load the packages
+# - display the sessionInfo
+loadAndDisplayPackages <- function(pkgs) {
+  for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
+
+  sessioninfo <- sessionInfo()
+  cat(sessioninfo$R.version$version.string, "\n")
+  cat("Main packages:\n")
+  for (pkg in names(sessioninfo$otherPkgs)) {
+    cat(paste(pkg, packageVersion(pkg)), "\t")
+  }
+  cat("\n")
+  cat("Other loaded packages:\n")
+  for (pkg in names(sessioninfo$loadedOnly)) {
+    cat(paste(pkg, packageVersion(pkg)), "\t")
+  }
+  cat("\n")
+}
+
+# This function retrieve a xset like object
+# @author Gildas Le Corguille lecorguille@sb-roscoff.fr
+getxcmsSetObject <- function(xobject) {
+  # XCMS 1.x
+  if (class(xobject) == "xcmsSet") {
+    return(xobject)
+  }
+  # XCMS 3.x
+  if (class(xobject) == "XCMSnExp") {
+    # Get the legacy xcmsSet object
+    suppressWarnings(xset <- as(xobject, "xcmsSet"))
+    if (is.null(xset@phenoData$sample_group)) {
+      sampclass(xset) <- "."
+    } else {
+      sampclass(xset) <- xset@phenoData$sample_group
+    }
+    if (!is.null(xset@phenoData$sample_name)) {
+      rownames(xset@phenoData) <- xset@phenoData$sample_name
+    }
+    return(xset)
+  }
+}
+
+# @author G. Le Corguille
+# The function create a pdf from the different png generated by diffreport
+diffreport_png2pdf <- function(filebase) {
+  dir.create("pdf")
+
+  pdfEicOutput <- paste0("pdf/", filebase, "-eic_pdf.pdf")
+  pdfBoxOutput <- paste0("pdf/", filebase, "-box_pdf.pdf")
+
+  system(paste0("gm convert ", filebase, "_eic/*.png ", pdfEicOutput))
+  system(paste0("gm convert ", filebase, "_box/*.png ", pdfBoxOutput))
+}
+
+# @author G. Le Corguille
+# The function create a zip archive from the different png generated by diffreport
+diffreport_png2zip <- function() {
+  zip("eic.zip", dir(pattern = "_eic"), zip = Sys.which("zip"))
+  zip("box.zip", dir(pattern = "_box"), zip = Sys.which("zip"))
+}
+
+# The function create a zip archive from the different tabular generated by diffreport
+diffreport_tabular2zip <- function() {
+  zip("tabular.zip", dir(pattern = "tabular/*"), zip = Sys.which("zip"))
+}
+
+# @author G. Le Corguille
+# This function convert if it is required the Retention Time in minutes
+RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
+  if (convertRTMinute) {
+    # converting the retention times (seconds) into minutes
+    print("converting the retention times into minutes in the variableMetadata")
+    variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
+    variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
+    variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
+  }
+  return(variableMetadata)
+}
+
+# @author G. Le Corguille
+# This function format ions identifiers
+formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
+  splitDeco <- strsplit(as.character(variableMetadata$name), "_")
+  idsDeco <- sapply(splitDeco, function(x) {
+    deco <- unlist(x)[2]
+    if (is.na(deco)) {
+      return("")
+    } else {
+      return(paste0("_", deco))
+    }
+  })
+  namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
+  variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
+  return(variableMetadata)
+}
+
+# The function annotateDiffreport without the corr function which bugs
+annotatediff <- function(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv") {
+  # Resolve the bug with x11, with the function png
+  options(bitmapType = "cairo")
+
+  # Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
+  res <- try(is.null(xset@filled))
+
+  # ------ annot -------
+  args$calcCiS <- as.logical(args$calcCiS)
+  args$calcIso <- as.logical(args$calcIso)
+  args$calcCaS <- as.logical(args$calcCaS)
+
+  # common parameters
+  args4annotate <- list(
+    object = xset,
+    nSlaves = args$nSlaves, sigma = args$sigma, perfwhm = args$perfwhm,
+    maxcharge = args$maxcharge, maxiso = args$maxiso, minfrac = args$minfrac,
+    ppm = args$ppm, mzabs = args$mzabs, quick = args$quick,
+    polarity = args$polarity, max_peaks = args$max_peaks, intval = args$intval
+  )
+
+  if (args$quick == FALSE) {
+    args4annotate <- append(
+      args4annotate,
+      list(
+        graphMethod = args$graphMethod, cor_eic_th = args$cor_eic_th, pval = args$pval,
+        calcCiS = args$calcCiS, calcIso = args$calcIso, calcCaS = args$calcCaS
+      )
+    )
+    # no ruleset
+    if (!is.null(args$multiplier)) {
+      args4annotate <- append(
+        args4annotate,
+        list(multiplier = args$multiplier)
+      )
+    } else {  # ruleset
+      rulset <- read.table(args$rules, h = TRUE, sep = ";")
+      if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = "\t")
+      if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = ",")
+      if (ncol(rulset) < 4) {
+        error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
+        print(error_message)
+        stop(error_message)
+      }
+
+      args4annotate <- append(
+        args4annotate,
+        list(rules = rulset)
+      )
+    }
+  }
+
+
+  # launch annotate
+  xa <- do.call("annotate", args4annotate)
+  peakList <- getPeaklist(xa, intval = args$intval)
+  peakList <- cbind(groupnames(xa@xcmsSet), peakList)
+  colnames(peakList)[1] <- c("name")
+
+  # --- Multi condition : diffreport ---
+  diffrepOri <- NULL
+  if (!is.null(args$runDiffreport) && nlevels(sampclass(xset)) >= 2) {
+    # Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
+    res <- try(is.null(xset@filled))
+    classes <- levels(sampclass(xset))
+    for (i in seq_len(length(classes) - 1)) {
+      for (n in seq_len(length(classes))) {
+        if (i + n <= length(classes)) {
+          filebase <- paste(classes[i], class2 = classes[i + n], sep = "-vs-")
+
+          diffrep <- diffreport(
+            object = xset, class1 = classes[i], class2 = classes[i + n],
+            filebase = filebase, eicmax = args$eicmax, eicwidth = args$eicwidth,
+            sortpval = TRUE, value = args$value, h = args$h, w = args$w, mzdec = args$mzdec, missing = 0
+          )
+
+          diffrepOri <- diffrep
+
+          # renamming of the column rtmed to rt to fit with camera peaklist function output
+          colnames(diffrep)[colnames(diffrep) == "rtmed"] <- "rt"
+          colnames(diffrep)[colnames(diffrep) == "mzmed"] <- "mz"
+
+          # combines results and reorder columns
+          diffrep <- merge(peakList, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = FALSE)
+          diffrep <- cbind(diffrep[, !(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))], diffrep[, (colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
+
+          diffrep <- RTSecondToMinute(diffrep, args$convertRTMinute)
+          diffrep <- formatIonIdentifiers(diffrep, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+
+          if (args$sortpval) {
+            diffrep <- diffrep[order(diffrep$pvalue), ]
+          }
+
+          dir.create("tabular", showWarnings = FALSE)
+          write.table(diffrep, sep = "\t", quote = FALSE, row.names = FALSE, file = paste("tabular/", filebase, "_tsv.tabular", sep = ""))
+
+          if (args$eicmax != 0) {
+            if (args$png2 == "pdf") {
+              diffreport_png2pdf(filebase)
+            }
+            if (args$png2 == "zip") {
+              diffreport_png2zip()
+            }
+          }
+        }
+      }
+    }
+    if (args$tabular2 == "zip") {
+      diffreport_tabular2zip()
+    }
+  }
+
+  # --- variableMetadata ---
+  variableMetadata <- peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
+  variableMetadata <- RTSecondToMinute(variableMetadata, args$convertRTMinute)
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+  # if we have 2 conditions, we keep stat of diffrep
+  if (!is.null(args$runDiffreport) && nlevels(sampclass(xset)) == 2) {
+    variableMetadata <- merge(variableMetadata, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = FALSE)
+    if (exists("args[[\"sortpval\"]]")) {
+      variableMetadata <- variableMetadata[order(variableMetadata$pvalue), ]
+    }
+  }
+
+  variableMetadataOri <- variableMetadata
+  write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
+
+  return(list("xa" = xa, "diffrep" = diffrepOri, "variableMetadata" = variableMetadataOri))
+}
+
+
+combinexsAnnos_function <- function(
+    xaP, xaN, diffrepP = NULL, diffrepN = NULL,
+    pos = TRUE, tol = 2, ruleset = NULL, keep_meta = TRUE, convertRTMinute = FALSE, numDigitsMZ = 0,
+    numDigitsRT = 0, variableMetadataOutput = "variableMetadata.tsv") {
+  # Load the two Rdata to extract the xset objects from positive and negative mode
+  cat("\tObject xset from positive mode\n")
+  print(xaP)
+  cat("\n")
+
+  cat("\tObject xset from negative mode\n")
+  print(xaN)
+  cat("\n")
+
+  cat("\n")
+  cat("\tCombining...\n")
+  # Convert the string to numeric for creating matrix
+  row <- as.numeric(strsplit(ruleset, ",")[[1]][1])
+  column <- as.numeric(strsplit(ruleset, ",")[[1]][2])
+  ruleset <- cbind(row, column)
+  # Test if the file comes from an older version tool
+  if ((!is.null(xaP)) && (!is.null(xaN))) {
+    # Launch the combinexsannos function from CAMERA
+    cAnnot <- combinexsAnnos(xaP, xaN, pos = pos, tol = tol, ruleset = ruleset)
+  } else {
+    stop("You must relauch the CAMERA.annotate step with the lastest version.")
+  }
+
+  if (pos) {
+    xa <- xaP
+    mode <- "neg. Mode"
+  } else {
+    xa <- xaN
+    mode <- "pos. Mode"
+  }
+
+  peakList <- getPeaklist(xa)
+  peakList <- cbind(groupnames(xa@xcmsSet), peakList)
+  colnames(peakList)[1] <- c("name")
+  variableMetadata <- cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup", mode)])
+  variableMetadata <- variableMetadata[, !(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
+
+  # Test if there are more than two classes (conditions)
+  if (nlevels(sampclass(xaP@xcmsSet)) == 2 && (!is.null(diffrepN)) && (!is.null(diffrepP))) {
+    diffrepP <- diffrepP[, c("name", "fold", "tstat", "pvalue")]
+    colnames(diffrepP) <- paste("P.", colnames(diffrepP), sep = "")
+    diffrepN <- diffrepN[, c("name", "fold", "tstat", "pvalue")]
+    colnames(diffrepN) <- paste("N.", colnames(diffrepN), sep = "")
+
+    variableMetadata <- merge(variableMetadata, diffrepP, by.x = "name", by.y = "P.name")
+    variableMetadata <- merge(variableMetadata, diffrepN, by.x = "name", by.y = "N.name")
+  }
+
+  rownames(variableMetadata) <- NULL
+  # TODO: checker colnames(variableMetadata)[1:2] = c("name", "mz/rt");
+
+  variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
+
+  # If the user want to keep only the metabolites which match a difference
+  if (keep_meta) {
+    variableMetadata <- variableMetadata[variableMetadata[, c(mode)] != "", ]
+  }
+
+  # Write the output into a tsv file
+  write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
+  return(variableMetadata)
+}
+
+# This function get the raw file path from the arguments
+getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
+  if (!is.null(args$zipfile)) zipfile <- args$zipfile
+  if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
+  if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
+
+  if (!is.null(args$singlefile_galaxyPath)) {
+    singlefile_galaxyPaths <- args$singlefile_galaxyPath
+    singlefile_sampleNames <- args$singlefile_sampleName
+  }
+  if (!is.null(args$singlefile_galaxyPathPositive)) {
+    singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive
+    singlefile_sampleNames <- args$singlefile_sampleNamePositive
+  }
+  if (!is.null(args$singlefile_galaxyPathNegative)) {
+    singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative
+    singlefile_sampleNames <- args$singlefile_sampleNameNegative
+  }
+  if (exists("singlefile_galaxyPaths")) {
+    singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, ","))
+    singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, ","))
+
+    singlefile <- NULL
+    for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
+      singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
+      singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
+      singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
+    }
+  }
+  for (argument in c(
+    "zipfile", "zipfilePositive", "zipfileNegative",
+    "singlefile_galaxyPath", "singlefile_sampleName",
+    "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
+    "singlefile_galaxyPathNegative", "singlefile_sampleNameNegative"
+  )) {
+    args[[argument]] <- NULL
+  }
+  return(list(zipfile = zipfile, singlefile = singlefile, args = args))
+}
+
+
+# This function retrieve the raw file in the working directory
+#   - if zipfile: unzip the file with its directory tree
+#   - if singlefiles: set symlink with the good filename
+retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile) {
+  if (!is.null(singlefile) && (length("singlefile") > 0)) {
+    for (singlefile_sampleName in names(singlefile)) {
+      singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
+      if (!file.exists(singlefile_galaxyPath)) {
+        error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
+        print(error_message)
+        stop(error_message)
+      }
+
+      file.symlink(singlefile_galaxyPath, singlefile_sampleName)
+    }
+    directory <- "."
+  }
+  if (!is.null(zipfile) && (zipfile != "")) {
+    if (!file.exists(zipfile)) {
+      error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
+      print(error_message)
+      stop(error_message)
+    }
+
+    # unzip
+    suppressWarnings(unzip(zipfile, unzip = "unzip"))
+
+    # get the directory name
+    filesInZip <- unzip(zipfile, list = TRUE)
+    directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
+    directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
+    directory <- "."
+    if (length(directories) == 1) directory <- directories
+
+    cat("files_root_directory\t", directory, "\n")
+  }
+  return(directory)
+}