Solves problem of creating variableMetadata with 1 sample

workflow4metabolomics · Nov 8, 2024 · 38cc94e · 38cc94e
1 parent 4e17f51
commit 38cc94e
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Showing 4 changed files with 64 additions and 88 deletions.
diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
@@ -138,27 +138,21 @@ print(xa)
 # Extract the list of annotated peaks
 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
-
-# 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(rownames(phenoData)) # Number of samples
-
-# Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols - 3) # 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 <- data.frame(
-  name = names_default,
-  name_custom = names_custom,
-  stringsAsFactors = FALSE
-)
-
-variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+if (length(phenoData@data$sample_name) == 1) {
+  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+} else {
+  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
+
+  variableMetadata <- data.frame(
+    name = names_default,
+    name_custom = names_custom,
+    stringsAsFactors = FALSE
+  )
+  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+}
 
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 

diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R
@@ -102,27 +102,21 @@ print(xa)
 # Extract the list of annotated peaks
 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
-
-# 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(rownames(phenoData)) # Number of samples
-
-# Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols - 3) # 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 <- data.frame(
-  name = names_default,
-  name_custom = names_custom,
-  stringsAsFactors = FALSE
-)
-
-variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+if (length(phenoData@data$sample_name) == 1) {
+  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+} else {
+  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
+
+  variableMetadata <- data.frame(
+    name = names_default,
+    name_custom = names_custom,
+    stringsAsFactors = FALSE
+  )
+  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+}
 
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 

diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R
@@ -109,27 +109,21 @@ print(xa)
 # Extract the list of annotated peaks
 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
-
-# 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(rownames(phenoData)) # Number of samples
-
-# Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols - 3) # 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 <- data.frame(
-  name = names_default,
-  name_custom = names_custom,
-  stringsAsFactors = FALSE
-)
-
-variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+if (length(phenoData@data$sample_name) == 1) {
+  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+} else {
+  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
+
+  variableMetadata <- data.frame(
+    name = names_default,
+    name_custom = names_custom,
+    stringsAsFactors = FALSE
+  )
+  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+}
 
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 

diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R
@@ -91,10 +91,10 @@ if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. O
 cat("Converting xset object to xsAnnotate...\n")
 xsa <- xsAnnotate(xset, sample = args$sample, nSlaves = as.numeric(args$nSlaves), polarity = args$polarity)
 
-print(paste0("All samples in xset object:", paste(seq_along(xset@filepaths), collapse = ", ")))
-print(paste0("Selected samples:", paste(xsa@sample, collapse = ", ")))
-print(paste0("Run in parallel mode (0 = disabled):", paste(xsa@runParallel)))
-print(paste0("Polarity:", xsa@polarity))
+print(paste0("All samples in xset object: ", paste(seq_along(xset@filepaths), collapse = ", ")))
+print(paste0("Selected samples: ", paste(xsa@sample, collapse = ", ")))
+print(paste0("Run in parallel mode (0 = disabled): ", paste(xsa@runParallel)))
+print(paste0("Polarity: ", xsa@polarity))
 
 # Apply the groupFWHM function with the parameters
 cat("Applying groupFWHM...\n")
@@ -103,27 +103,21 @@ xa <- groupFWHM(xsa, sigma = as.numeric(args$sigma), perfwhm = as.numeric(args$p
 # Extract the list of annotated peaks
 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
-
-# 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(rownames(xdata@phenoData)) # Number of samples
-
-# Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols - 3) # 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 <- data.frame(
-  name = names_default,
-  name_custom = names_custom,
-  stringsAsFactors = FALSE
-)
-
-variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+if (length(phenoData@data$sample_name) == 1) {
+  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+} else {
+  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
+
+  variableMetadata <- data.frame(
+    name = names_default,
+    name_custom = names_custom,
+    stringsAsFactors = FALSE
+  )
+  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+}
 
 if (!exists("RTinMinute")) RTinMinute <- FALSE