From 1d3e4824bda0633af3516f2d9cd8f9d976884767 Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Thu, 21 Nov 2024 11:04:56 +0100
Subject: [PATCH] update code chromPeakSpectra()

---
 R/XcmsExperiment-functions.R | 21 ++++++++++++++-------
 R/XcmsExperiment.R           | 19 +++++++++++++------
 2 files changed, 27 insertions(+), 13 deletions(-)

diff --git a/R/XcmsExperiment-functions.R b/R/XcmsExperiment-functions.R
index c8366696..be67d750 100644
--- a/R/XcmsExperiment-functions.R
+++ b/R/XcmsExperiment-functions.R
@@ -793,7 +793,9 @@
                                                  "largest_bpi"),
                                    msLevel = 2L, expandRt = 0, expandMz = 0,
                                    ppm = 0, skipFilled = FALSE,
-                                   peaks = integer(), peaksInfo = c("rt", "mz"),
+                                   peaks = integer(),
+                                   addColumnsChromPeaks = c("rt", "mz"),
+                                   addColumnsChrompeaksPrefix = "chrom_peak_",
                                    BPPARAM = bpparam()) {
     method <- match.arg(method)
     pks <- .chromPeaks(x)[, c("mz", "mzmin", "mzmax", "rt",
@@ -819,7 +821,8 @@
     res <- bpmapply(
         split.data.frame(pks, f),
         split(spectra(x), factor(fromFile(x), levels = levels(f))),
-        FUN = function(pk, sp, msLevel, method) {
+        FUN = function(pk, sp, msLevel, method, addColumnsChromPeaks,
+                       addColumnsChrompeaksPrefix) {
             sp <- filterMsLevel(sp, msLevel)
             idx <- switch(
                 method,
@@ -830,13 +833,17 @@
                 largest_bpi = .spectra_index_list_largest_bpi(sp, pk, msLevel))
             ids <- rep(rownames(pk), lengths(idx))
             res <- sp[unlist(idx)]
-            res$peak_id <- ids
-            info <- pk[res$peak_id, peaksInfo]
-            colnames(info) <- paste("peak_", peaksInfo, sep = "")
-            res@backend@spectraData <- cbind(res@backend@spectraData, info)
+            pk_data <- DataFrame(pk[ids, addColumnsChromPeaks, drop = FALSE])
+            pk_data$id <- ids
+            colnames(pk_data) <- paste0(addColumnsChrompeaksPrefix,
+                                          colnames(pk_data))
+            pk_data$spectrumId <- res$spectrumId
+            res <- Spectra::joinSpectraData(res, pk_data)
             res
         },
-        MoreArgs = list(msLevel = msLevel, method = method),
+        MoreArgs = list(msLevel = msLevel, method = method,
+                        addColumnsChromPeaks = addColumnsChromPeaks,
+                        addColumnsChrompeaksPrefix = addColumnsChrompeaksPrefix),
         BPPARAM = BPPARAM)
     Spectra:::.concatenate_spectra(res)
 }
diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
index c695da70..1cbb8545 100644
--- a/R/XcmsExperiment.R
+++ b/R/XcmsExperiment.R
@@ -1232,7 +1232,9 @@ setMethod(
     function(object, method = c("all", "closest_rt", "closest_mz",
                                 "largest_tic", "largest_bpi"),
              msLevel = 2L, expandRt = 0, expandMz = 0, ppm = 0,
-             skipFilled = FALSE, peaks = character(), peaksInfo = c("rt", "mz"),
+             skipFilled = FALSE, peaks = character(),
+             addColumnsChromPeaks = c("rt", "mz"),
+             addColumnsChromPeaksPrefix = "chrom_peak_",
              return.type = c("Spectra", "List"), BPPARAM = bpparam()) {
         if (hasAdjustedRtime(object))
             object <- applyAdjustedRtime(object)
@@ -1248,14 +1250,19 @@ setMethod(
         else pkidx <- integer()
         res <- .mse_spectra_for_peaks(object, method, msLevel, expandRt,
                                       expandMz, ppm, skipFilled, pkidx,
-                                      peaksInfo, BPPARAM)
+                                      addColumnsChromPeaks,
+                                      addColumnsChromPeaksPrefix,
+                                      BPPARAM)
         if (!length(pkidx))
             peaks <- rownames(.chromPeaks(object))
         else peaks <- rownames(.chromPeaks(object))[pkidx]
-        if (return.type == "Spectra")
-            res <- res[as.matrix(findMatches(peaks, res$peak_id))[, 2L]]
-        else
-            as(split(res, factor(res$peak_id, levels = peaks)), "List")
+        if (return.type == "Spectra") {
+            col <- paste0(addColumnsChromPeaksPrefix, "id")
+            res <- res[as.matrix(findMatches(peaks, res[[col]]))[, 2L]]
+        } else {
+            col <- paste0(addColumnsChromPeaksPrefix, "id")
+            as(split(res, factor(res[[col]], levels = peaks)), "List")
+        }
     })
 
 #' @rdname reconstructChromPeakSpectra