addition of addCollmns.. parameters and documentation

Author: philouail

Diff for: R/AllGenerics.R

@@ -411,14 +411,21 @@ setGeneric("chromPeakData<-", function(object, value)
 #'
 #' Parameter `return.type` allows to specify the *type* of the result object.
 #' With `return.type = "Spectra"` (the default) a [Spectra] object with all
-#' matching spectra is returned. The spectra variable `"peak_id"` of the
-#' returned `Spectra` contains the ID of the chromatographic peak (i.e., the
-#' rowname of the peak in the `chromPeaks` matrix) for each spectrum.
-#' With `return.type = "Spectra"` a `List` of `Spectra` is returned. The
-#' length of the list is equal to the number of rows of `chromPeaks`. Each
-#' element of the list contains thus a `Spectra` with all spectra for one
-#' chromatographic peak (or a `Spectra` of length 0 if no spectrum was found
-#' for the respective chromatographic peak).
+#' matching spectra is returned. With `return.type = "Spectra"` a `List` of
+#' `Spectra` is returned. The length of the list is equal to the number of rows
+#' of `chromPeaks`. Each element of the list contains thus a `Spectra` with all
+#' spectra for one chromatographic peak (or a `Spectra` of length 0 if no
+#' spectrum was found for the respective chromatographic peak).
+#'
+#' Parameters `addColumnsChromPeaks` allow the user to add specific metadata
+#' columns from the chromatographic peaks (`chromPeaks`) to the returned
+#' spectra object. This can be useful to retain information such as retention
+#' time (`rt`), m/z (`mz`). The columns will be named as they is written in the
+#' `chromPeaks` object with a prefix that is defined by the parameter
+#' `addColumnsChromPeaksPrefix`. The *peak ID* (i.e., the row name of the
+#' peak in the `chromPeaks` matrix) is always added to the spectra object as
+#' metadata column `paste0(addColumnsChromPeaksPrefix,id)`, by default it will
+#' be `"chrom_peak_id"`.
 #'
 #' See also the *LC-MS/MS data analysis* vignette for more details and examples.
 #'
@@ -453,6 +460,16 @@ setGeneric("chromPeakData<-", function(object, value)
 #' @param return.type `character(1)` defining the type of result object that
 #'     should be returned.
 #'
+#' @param addColumnsChromPeaks `character` vector with the names of the columns
+#'    from `chromPeaks` that should be added to the returned spectra object.
+#'    The columns will be named as they are written in the `chromPeaks` object
+#'    with a prefix that is defined by the parameter
+#'    `addColumnsChromPeaksPrefix`. Defaults to `c("mz", "rt")`.
+#'
+#' @param addColumnsChromPeaksPrefix `character(1)` defining the prefix that
+#'    should be used for the columns from `chromPeaks` that are added to the
+#'    returned spectra object. Defaults to `"chrom_peak_"`.
+#'
 #' @param BPPARAM parallel processing setup. Defaults to [bpparam()].
 #'
 #' @param ... ignored.
@@ -503,7 +520,7 @@ setGeneric("chromPeakData<-", function(object, value)
 #' ## spectra variable *peak_id* contain the row names of the peaks in the
 #' ## chromPeak matrix and allow thus to map chromatographic peaks to the
 #' ## returned MS2 spectra
-#' ms2_sps$peak_id
+#' ms2_sps$chrom_peak_id
 #' chromPeaks(dda)
 #'
 #' ## Alternatively, return the result as a List of Spectra objects. This list
@@ -799,10 +816,24 @@ setGeneric("featureDefinitions<-", function(object, value)
 #' spectrum **per chromatographic peak** will be returned (hence multiple
 #' spectra per feature).
 #'
-#' The ID of each chromatographic peak (i.e. its row name in `chromPeaks`)
-#' and each feature (i.e., its row name in `featureDefinitions`) are
-#' available in the returned [Spectra()] with spectra variables `"peak_id"`
-#' and `"feature_id"`, respectively.
+#' The information from `featureDefinitions` for each feature can be included
+#' in the returned [Spectra()] object using the `addColumnsFeatures` parameter.
+#' This is useful for retaining details such as the median retention time (`rtmed`)
+#' or median m/z (`mzmed`). The columns will retain their names as specified
+#' in the `featureDefinitions` object, prefixed by the value of the
+#' `addColumnsFeaturesPrefix` parameter. Additionally, the *feature ID*
+#' (i.e., the row name of the feature in the `featureDefinitions` data.frame)
+#' is always added as a metadata column with the name
+#' `paste0(addColumnsFeaturesPrefix, "id")`, which defaults to `"feature_id"`.
+#'
+#' See also [chromPeakSpectra()], as it supports a similar parameter for
+#' including columns from the chromatographic peaks in the returned spectra object.
+#' These parameters can be used in combination to include information from both
+#' the chromatographic peaks and the features in the returned [Spectra()].
+#' The *peak ID* (i.e., the row name of the peak in the `chromPeaks` matrix)
+#' is added as a metadata column with the name
+#' `paste0(addColumnsChromPeaksPrefix, "id")`, which defaults to
+#' `"chrom_peak_id"`.
 #'
 #' @param object [XcmsExperiment] or [XCMSnExp] object with feature defitions.
 #'
@@ -815,6 +846,16 @@ setGeneric("featureDefinitions<-", function(object, value)
 #'     `featureDefinitions(x)`). This parameter overrides `skipFilled` and is
 #'     only supported for `return.type` being either `"Spectra"` or `"List"`.
 #'
+#' @param addColumnsFeatures `character` vector with the names of the columns
+#'     from `featureDefinitions` that should be added to the returned spectra
+#'     object. The columns will be named as they are written in the
+#'    `featureDefinitions` object with a prefix that is defined by the parameter
+#'    `addColumnsFeaturesPrefix`. Defaults to `c("mzmed", "rtmed")`.
+#'
+#' @param addColumnsFeaturesPrefix `character(1)` defining the prefix that
+#'     should be used for the columns from `featureDefinitions` that are added
+#'     to the returned spectra object. Defaults to `"feature_"`.
+#'
 #' @param ... additional arguments to be passed along to [chromPeakSpectra()],
 #'     such as `method`.
 #'

Diff for: R/XcmsExperiment-functions.R

@@ -795,7 +795,7 @@
                                    ppm = 0, skipFilled = FALSE,
                                    peaks = integer(),
                                    addColumnsChromPeaks = c("rt", "mz"),
-                                   addColumnsChrompeaksPrefix = "chrom_peak_",
+                                   addColumnsChromPeaksPrefix = "chrom_peak_",
                                    BPPARAM = bpparam()) {
     method <- match.arg(method)
     pks <- .chromPeaks(x)[, c("mz", "mzmin", "mzmax", "rt",
@@ -822,8 +822,8 @@
         split.data.frame(pks, f),
         split(spectra(x), factor(fromFile(x), levels = levels(f))),
         FUN = function(pk, sp, msLevel, method, addColumnsChromPeaks,
-                       addColumnsChrompeaksPrefix) {
-            sp <- filterMsLevel(sp, msLevel)
+                       addColumnsChromPeaksPrefix) {
+            sp <- Spectra::filterMsLevel(sp, msLevel)
             idx <- switch(
                 method,
                 all = .spectra_index_list(sp, pk, msLevel),
@@ -833,21 +833,37 @@
                 largest_bpi = .spectra_index_list_largest_bpi(sp, pk, msLevel))
             ids <- rep(rownames(pk), lengths(idx))
             res <- sp[unlist(idx)]
-            pk_data <- DataFrame(pk[ids, addColumnsChromPeaks, drop = FALSE])
-            pk_data$id <- ids
-            colnames(pk_data) <- paste0(addColumnsChrompeaksPrefix,
+            pk_data <- pk[ids, addColumnsChromPeaks, drop = FALSE]
+            pk_data <- cbind(pk_data, id = ids)
+            colnames(pk_data) <- paste0(addColumnsChromPeaksPrefix,
                                           colnames(pk_data))
-            pk_data$spectrumId <- res$spectrumId
-            res <- Spectra::joinSpectraData(res, pk_data)
+            res <- .add_spectra_data(res, pk_data)
             res
         },
         MoreArgs = list(msLevel = msLevel, method = method,
                         addColumnsChromPeaks = addColumnsChromPeaks,
-                        addColumnsChrompeaksPrefix = addColumnsChrompeaksPrefix),
+                        addColumnsChromPeaksPrefix = addColumnsChromPeaksPrefix),
         BPPARAM = BPPARAM)
     Spectra:::.concatenate_spectra(res)
 }
 
+#' @param x `Spectra` object.
+#'
+#' @param data `data.frame` or `matrix` with the data to be added to the
+#'     spectra object.
+#'
+#' @noRd
+.add_spectra_data <- function(x, data) {
+    if (is(data, "matrix"))
+        data <- as.data.frame(data)
+    if (nrow(data) != length(x))
+        stop("Length of 'data' does not match the number of spectra in 'x'")
+    for (i in colnames(data)) {
+        x[[i]] <- data[, i]
+    }
+    x
+}
+
 #' @param peaks `matrix` with chrom peaks.
 #'
 #' @param peakIdx `list` of `integer` indices defining which chromatographic

Diff for: R/XcmsExperiment.R

@@ -515,10 +515,6 @@
 #'     indicating the identified chromatographic peaks. Only a single color
 #'     is supported. Defaults to `peakCol = "#ff000060".
 #'
-#' @param peaksInfo For `chromPeakSpectra`: `character`  vector of additional
-#'    information from `chromPeaks()` to be added to the spectra object. The
-#'    columns names will be appended with "peaks_".
-#'
 #' @param ppm For `chromPeaks` and `featureDefinitions`: optional `numeric(1)`
 #'     specifying the ppm by which the m/z range (defined by `mz` should be
 #'     extended. For a value of `ppm = 10`, all peaks within `mz[1] - ppm / 1e6`
@@ -1784,7 +1780,11 @@ setMethod(
     "featureSpectra", "XcmsExperiment",
     function(object, msLevel = 2L, expandRt = 0, expandMz = 0, ppm = 0,
              skipFilled = FALSE, return.type = c("Spectra", "List"),
-             features = character(), ...) {
+             features = character(),
+             addColumnsFeatures = c("rtmed", "mzmed"),
+             addColumnsFeaturesPrefix = "feature_",
+             addColumnsChromPeaksPrefix = "chrom_peak_",
+             ...) {
         return.type <- match.arg(return.type)
         if (!hasFeatures(object))
             stop("No feature definitions present. Please run ",
@@ -1803,13 +1803,18 @@ setMethod(
         sps <- .mse_spectra_for_peaks(
             object, msLevel = msLevel, expandRt = expandRt,
             expandMz = expandMz, ppm = ppm, skipFilled = skipFilled,
-            peaks = unique(pindex), ...)
+            peaks = unique(pindex),
+            addColumnsChromPeaksPrefix = addColumnsChromPeaksPrefix)
+        col <- paste0(addColumnsChromPeaksPrefix, "id")
         mtch <- as.matrix(
-            findMatches(sps$peak_id, rownames(.chromPeaks(object))[pindex]))
+            findMatches(sps[[col]], rownames(.chromPeaks(object))[pindex]))
         sps <- sps[mtch[, 1L]]
         fid <- rep(
             ufeatures, lengths(featureDefinitions(object)$peakidx[findex]))
-        sps$feature_id <- fid[mtch[, 2L]]
+        f_data <- featureDefinitions(object)[fid[mtch[, 2L]], addColumnsFeatures]
+        f_data$id <- fid[mtch[, 2L]]
+        colnames(f_data) <- paste0(addColumnsFeaturesPrefix, colnames(f_data))
+        sps <- .add_spectra_data(sps, f_data)
         if (return.type == "List") {
             sps <- List(split(sps, f = factor(sps$feature_id,
                                               levels = ufeatures)))