Move to BiocParallel

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "editor.rulers": [
+    80, 120
+    ]
+}

DESCRIPTION

@@ -12,8 +12,6 @@ Description: An automated pipeline for the detection, integration and reporting
 Depends:
 	R (>= 4.2)
 Imports: 
-	foreach (>= 1.4.4),
-	doParallel (>= 1.0.11),
 	ggplot2 (>= 3.5.0),
 	gridExtra (>= 2.3),
 	MSnbase (>= 2.4.0),
@@ -28,6 +26,7 @@ Imports:
 	shinycssloaders (>= 1.0.0),
 	DT (>= 0.15),
 	pracma (>= 2.2.3),
+	BiocParallel (>= 1.28.3),
 	utils,
 	lubridate,
 	svglite (>= 2.1.1)

NAMESPACE

@@ -49,9 +49,8 @@ exportMethods(uROI)
 exportMethods(uROIExist)
 exportMethods(useFIR)
 exportMethods(useUROI)
+import(BiocParallel)
 import(XML)
-import(doParallel)
-import(foreach)
 import(methods)
 import(mzR)
 import(scales)

R/methods_peakPantheRAnnotation.R

@@ -1598,7 +1598,7 @@ singleDiagnosticPlots <- function(tmp_annotation,sampleColour,sampling,verbose){
 ## fitted compound
 setGeneric("outputAnnotationDiagnostic",
     function(object, saveFolder, savePlots = TRUE, sampleColour = NULL,
-            verbose = TRUE, ncores = 0, svgPlot = FALSE, ...)
+            verbose = TRUE, nCores = 1, BPPARAM=NULL, svgPlot = FALSE, ...)
     standardGeneric("outputAnnotationDiagnostic"))
 #' @title Save to disk the annotation parameters as CSV and a diagnostic plot
 #' per fitted compound
@@ -1612,7 +1612,9 @@ setGeneric("outputAnnotationDiagnostic",
 #' @param savePlots (bool) If TRUE save a diagnostic plot for each compound
 #' @param sampleColour (str) NULL or vector colour for each sample
 #' @param verbose (bool) If TRUE message progress
-#' @param ncores (int) Number of cores to use to save plots in parallel
+#' @param nCores (int) Number of cores to use to save plots in parallel
+#' @param BPPARAM (BiocParallel::BiocParallelParam) Settings for parallel
+#' processing. Must be a BiocParallelParam object
 #' @param svgPlot (bool) If TRUE save plots as 'svg', otherwise as 'png'
 #' @param ... Additional parameters for plotting i.e. \code{sampling} for the
 #' number of points to employ when plotting fittedCurve
@@ -1647,7 +1649,7 @@ setGeneric("outputAnnotationDiagnostic",
 #'                                         targetFeatTable=targetFeatTable)
 #'
 #' # Calculate annotation
-#' annotation <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
+#' annotation <- peakPantheR_parallelAnnotation(emptyAnnotation, nCores=1,
 #'                                 getAcquTime=FALSE, verbose=FALSE)$annotation
 #'
 #' # temporary location
@@ -1656,8 +1658,8 @@ setGeneric("outputAnnotationDiagnostic",
 #'                             verbose=TRUE)
 #' }
 setMethod("outputAnnotationDiagnostic", "peakPantheRAnnotation",
-    function(object, saveFolder, savePlots, sampleColour, verbose, ncores,
-            svgPlot,...) {
+    function(object, saveFolder, savePlots, sampleColour, verbose, nCores,
+            BPPARAM, svgPlot, ...) {
     # Save standardised csv
     outputAnnotationParamsCSV(object, saveFolder = saveFolder,verbose = verbose)
 
@@ -1668,23 +1670,41 @@ setMethod("outputAnnotationDiagnostic", "peakPantheRAnnotation",
         nbCpd <- nbCompounds(object)
 
         # run in parallel
-        if (ncores > 0) {
-            if (verbose) {
-                message("Saving ", nbCpd, " diagnostic plots in ", saveFolder) }
-
-            # Open parallel interface
-            cl <- parallel::makeCluster(ncores)
-            doParallel::registerDoParallel(cl)
-            # Run
-            savedPlots <- foreach::foreach(x = seq_len(nbCpd),
-                                            .inorder = TRUE) %dopar%
-                outputAnnotationDiagnostic_saveSingleMultiPlot(cpdNb = x,
-                    annotation = object, saveFolder = saveFolder,
-                    sampleColour = sampleColour, nbCpd = nbCpd,
-                    verbose = verbose, svgPlot = svgPlot, ...)
-            # Close
-            parallel::stopCluster(cl)
-            if (verbose) { message("All plots saved") }
+        nCores <- as.integer(nCores)
+        if (nCores < 0) {
+            stop("Check input, nCores must be a positive integer")
+        }
+        # Handle default BPParam
+        if (is.null(BPPARAM)) {
+            if (nCores > 1) {
+                if (.Platform$OS.type == 'windows') {
+                BPPARAM <- BiocParallel::SnowParam(workers = nCores)
+                }
+                else {
+                BPPARAM <- BiocParallel::MulticoreParam(workers = nCores)
+                }
+            } else {
+            BPPARAM <- BiocParallel::SerialParam()}
+        }
+        else if (!is(BPPARAM, 'BiocParallelParam')) {
+            stop("Check input, BPPARAM must be a BiocParallel Param object")
+        }
+
+        if (verbose) {
+            message("Saving ", nbCpd, " diagnostic plots in ", saveFolder) }
+
+        # Open parallel interface
+        BiocParallel::register(BPPARAM)
+        BiocParallel::bpstart(BPPARAM)
+        # Run
+        savedPlots <- BiocParallel::bplapply(X=seq_len(nbCpd),
+                FUN = outputAnnotationDiagnostic_saveSingleMultiPlot,
+                annotation = object, saveFolder = saveFolder,
+                sampleColour = sampleColour, nbCpd = nbCpd,
+                verbose = verbose, BPPARAM = BPPARAM, svgPlot = svgPlot, ...)
+        # Close parallel interface
+        BiocParallel::bpstop(BPPARAM)
+        if (verbose) { message("All plots saved") }
 
         # run serial
         } else {
@@ -1794,7 +1814,7 @@ setGeneric("outputAnnotationResult",
 #'                                         targetFeatTable=targetFeatTable)
 #'
 #' # Calculate annotation
-#' annotation      <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
+#' annotation      <- peakPantheR_parallelAnnotation(emptyAnnotation, nCores=1,
 #'                                 getAcquTime=FALSE, verbose=FALSE)$annotation
 #'
 #' # temporary location
@@ -2437,7 +2457,7 @@ setGeneric("retentionTimeCorrection",
 #'                                         targetFeatTable=targetFeatTable)
 #' # annotate files serially
 #' annotation_result <- peakPantheR_parallelAnnotation(smallAnnotation,
-#'                                          ncores=0, verbose=TRUE)
+#'                                          nCores=1, verbose=TRUE)
 #' data_annotation   <- annotation_result$annotation
 #'
 #' # Example with constant correction

R/peakPantheR.R

@@ -47,8 +47,7 @@
 #' @docType package
 #' @name peakPantheR
 #'
-#' @import foreach
-#' @import doParallel
+#' @import BiocParallel
 #'
 "_PACKAGE"
 #> [1] "_PACKAGE"

R/peakPantheR_ROIStatistics.R

@@ -17,7 +17,9 @@
 #' (float), \code{mz} (float or \emph{NA}), \code{mzMax} (float)  (if NULL IS
 #' mean RT is not calculated and saved in \code{IS_mean_RT.csv})
 #' @param sampleColour (str) NULL or vector colour for each sample
-#' @param ncores (int) Number of cores to use to integrate IS in parallel
+#' @param nCores (int) Number of cores to use to integrate IS in parallel
+#' @param BPPARAM (BiocParallel::BiocParallelParam) Settings for parallel 
+#' processing. Must be a BiocParallelParam object
 #' @param saveISPlots (bool) If TRUE save a diagnostic plot for each IS to
 #' \code{saveFolder/IS_search} compound
 #' @param verbose (bool) If TRUE message progress
@@ -54,12 +56,13 @@
 #' # Calculate ROI statiscs
 #' peakPantheR_ROIStatistics(refSpecFiles, saveFolder1, ROI=input_ROI,
 #'                             IS_ROI=input_IS_ROI, sampleColour=sampleColour,
-#'                             ncores=0, saveISPlots=TRUE, verbose=TRUE)
+#'                             nCores=1, saveISPlots=TRUE, verbose=TRUE)
 #' }
 peakPantheR_ROIStatistics   <- function(referenceSpectraFiles, saveFolder,
                                         ROI = NULL, IS_ROI = NULL,
-                                        sampleColour = NULL, ncores = 0,
-                                        saveISPlots = TRUE, verbose = TRUE) {
+                                        sampleColour = NULL, nCores = 1,
+                                        saveISPlots = TRUE, verbose = TRUE, 
+                                        BPPARAM=NULL) {
     # Check and process input parameters
     resInit <- ROIStatistics_init_checks(referenceSpectraFiles, saveFolder, ROI,
                                         IS_ROI, sampleColour, verbose)
@@ -77,7 +80,7 @@ peakPantheR_ROIStatistics   <- function(referenceSpectraFiles, saveFolder,
     # calculate mean IS for each RT
     if (calculateMeanISRT) {
         ROIStatistics_calculateMeanISRT(referenceSpectraFiles, saveFolder,
-                            IS_ROI, saveISPlots, ncores, sampleColour, verbose)
+                IS_ROI, saveISPlots, nCores, sampleColour, verbose, BPPARAM)
     }
 }
 
@@ -239,23 +242,23 @@ ROIStatistics_saveEICsROI <- function(referenceSpectraFiles, saveFolder, ROI,
 }
 # Calculate mean RT for each IS
 ROIStatistics_calculateMeanISRT <- function(referenceSpectraFiles, saveFolder,
-                            IS_ROI, saveISPlots, ncores, sampleColour, verbose){
+                IS_ROI, saveISPlots, nCores, sampleColour, verbose, BPPARAM){
     if (verbose) {
         message("\n-- Calculating mean RT for each IS --")
     }
     IS_annotation <- peakPantheRAnnotation(
         spectraPaths = referenceSpectraFiles,
         targetFeatTable = IS_ROI)
     IS_annotation_results <- peakPantheR_parallelAnnotation(IS_annotation,
-        ncores = ncores, verbose = verbose)
+        nCores = nCores, verbose = verbose, BPPARAM=BPPARAM)
     IS_annotation <- IS_annotation_results$annotation
 
     # save IS fit diagnostic plots
     if (saveISPlots) {
         outputAnnotationDiagnostic(IS_annotation,
             saveFolder = file.path(saveFolder, "IS_search"),
             savePlots = TRUE, sampleColour=sampleColour, verbose = verbose,
-            ncores = ncores)
+            nCores = nCores)
     }
 
     # calculate statistics