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Code indentation for R files
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@DamienCode404
DamienCode404 committed Oct 18, 2024
1 parent 9ebb51a commit 52883bb
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Showing 4 changed files with 390 additions and 392 deletions.
198 changes: 98 additions & 100 deletions tools/camera/CAMERA_findAdducts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -12,39 +12,38 @@ print(args_vec)

# Function to convert "NULL" strings to actual NULL values
convertNullString <- function(x) {
if (x == "NULL") {
return(NULL)
}
return(x)
if (x == "NULL") {
return(NULL)
}
return(x)
}

args <- list(
image = args_vec[1], # the xsAnnotate object
ppm = as.numeric(args_vec[2]), # ppm error for the search
mzabs = as.numeric(args_vec[3]), # allowed variance for the search
multiplier = as.numeric(args_vec[4]), # highest number(n) of allowed clusterion [nM+ion]
polarity = args_vec[5], # Which polarity mode was used for measuring of the MS sample
rules = args_vec[6], # custom ruleset or NULL for default ruleset
max_peaks = as.numeric(args_vec[7]), # If run in parallel mode, this number defines how many peaks will be calculated in each thread
psg_list = convertNullString(args_vec[8]), # Vector of pseudospectra indices; correlation analysis will only be done for those groups
intval = args_vec[9], # choose intensity values. Allowed values are "into", "maxo", "intb" (string)
convertRTMinute = as.logical(args_vec[10]), # TRUE - FALSE
numDigitsMZ = as.numeric(args_vec[11]), # Number of digits MZ
numDigitsRT = as.numeric(args_vec[12]) # Number of digits RT
image = args_vec[1], # the xsAnnotate object
ppm = as.numeric(args_vec[2]), # ppm error for the search
mzabs = as.numeric(args_vec[3]), # allowed variance for the search
multiplier = as.numeric(args_vec[4]), # highest number(n) of allowed clusterion [nM+ion]
polarity = args_vec[5], # Which polarity mode was used for measuring of the MS sample
rules = args_vec[6], # custom ruleset or NULL for default ruleset
max_peaks = as.numeric(args_vec[7]), # If run in parallel mode, this number defines how many peaks will be calculated in each thread
psg_list = convertNullString(args_vec[8]), # Vector of pseudospectra indices; correlation analysis will only be done for those groups
intval = args_vec[9], # choose intensity values. Allowed values are "into", "maxo", "intb" (string)
convertRTMinute = as.logical(args_vec[10]), # TRUE - FALSE
numDigitsMZ = as.numeric(args_vec[11]), # Number of digits MZ
numDigitsRT = as.numeric(args_vec[12]) # Number of digits RT
)

# Convert "NULL" to actual NULL or convert to data frame
if (args$rules == "NULL") {
args$rulset <- convertNullString(args$rules) # Return NULL
args$rulset <- convertNullString(args$rules) # Return NULL
} else {
args$rulset <- read.table(args$rules, h = TRUE, sep = ",")
if (ncol(args$rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = "\t")
if (ncol(args$rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = ",")
if (ncol(args$rulset) < 4) {
error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
print(error_message)
stop(error_message)
}
if (ncol(args$rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = "\t")
if (ncol(args$rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = ",")
if (ncol(args$rulset) < 4) {
error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
print(error_message)
stop(error_message)
}
}

print("Converted arguments:")
Expand All @@ -55,7 +54,7 @@ print(sapply(args, class))

# Verify the arguments
if (!file.exists(args$image)) {
stop("The provided RData file does not exist: ", args$image)
stop("The provided RData file does not exist: ", args$image)
}

# Load the RData file
Expand All @@ -64,42 +63,42 @@ args$image <- NULL

# Function to retrieve the raw file 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))
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))
}

# Save arguments for report generation
Expand All @@ -114,33 +113,33 @@ args <- rawFilePath$args

# Function to retrieve raw files in the working directory
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 at:", singlefile_galaxyPath)
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)
print(error_message)
stop(error_message)
}
suppressWarnings(unzip(zipfile, unzip = "unzip"))
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)
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 at:", singlefile_galaxyPath)
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)
print(error_message)
stop(error_message)
}
suppressWarnings(unzip(zipfile, unzip = "unzip"))
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)
}

# Retrieve the files
Expand All @@ -161,15 +160,15 @@ RTSecondToMinute <- function(variableMetadata, convertRTMinute) {

# Verify that the object xa is loaded
if (!exists("xa")) {
stop("The object xa was not found in the RData file.")
stop("The object xa was not found in the RData file.")
}

print("Loaded xa object:")
print(xa)

# Apply the findAdducts function on the xsAnnotate object
print("Calling findAdducts function:")
xa <- findAdducts(xa, ppm=args$ppm, mzabs=args$mzabs, multiplier=args$multiplier, polarity=args$polarity, rules=args$rulset, max_peaks=args$max_peaks, psg_list=args$psg_list, intval=args$intval)
xa <- findAdducts(xa, ppm = args$ppm, mzabs = args$mzabs, multiplier = args$multiplier, polarity = args$polarity, rules = args$rulset, max_peaks = args$max_peaks, psg_list = args$psg_list, intval = args$intval)

print("Result of findAdducts function:")
print(xa)
Expand All @@ -178,17 +177,17 @@ print(xa)
peakList <- getPeaklist(xa, intval = args$intval)

# Generate group names with and without decimals for mz and rt
names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ , rtdec = args$numDigitsRT) # Names with "x" decimals
names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals

# Calculate indices of the columns to include from peakList
# Select all columns except the last sample-specific columns
ncols <- length(colnames(peakList))
sample_cols <- length(xa@sample) # Number of samples
sample_cols <- length(xa@sample) # Number of samples

# Indices for the columns of interest
main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)

# Combine the selected columns from matgrp with the group names
variableMetadata <- cbind(
Expand All @@ -200,18 +199,17 @@ variableMetadata <- cbind(
if (!exists("RTinMinute")) RTinMinute <- FALSE

if (args$convertRTMinute && RTinMinute == FALSE) {
RTinMinute <- TRUE
variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
RTinMinute <- TRUE
variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
}

# Save the extracted peak list as a TSV file named 'variableMetadata.tsv'
output_file_tsv <- "variableMetadata.tsv"
write.table(variableMetadata, file=output_file_tsv, sep = "\t", row.names = FALSE, quote = FALSE)
write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FALSE, quote = FALSE)

# Save the updated xsAnnotate object
output_file_RData <- "camera_findAdducts.RData"
objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute")
save(list = objects2save[objects2save %in% ls()], file = output_file_RData)

cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")

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