Add default charge up to precursor charge in plotSpectraPTM

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PSMatch
 Title: Handling and Managing Peptide Spectrum Matches
-Version: 1.15.3
+Version: 1.17.1
 Authors@R:
    c(person(given = "Laurent", family = "Gatto",
             email = "laurent.gatto@uclouvain.be",
@@ -61,8 +61,9 @@ Suggests:
 License: Artistic-2.0
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 BugReports: https://github.com/RforMassSpectrometry/PSM/issues
 URL: https://github.com/RforMassSpectrometry/PSM
 biocViews: Infrastructure, Proteomics, MassSpectrometry
+Config/roxygen2/version: 8.0.0
+RoxygenNote: 7.3.3

NAMESPACE

@@ -54,6 +54,7 @@ importFrom(ProtGenerics,adjacencyMatrix)
 importFrom(ProtGenerics,calculateFragments)
 importFrom(QFeatures,reduceDataFrame)
 importFrom(Spectra,peaksData)
+importFrom(Spectra,precursorCharge)
 importFrom(Spectra,spectraData)
 importFrom(Spectra,spectraVariables)
 importFrom(grDevices,n2mfrow)

NEWS.md

@@ -1,5 +1,14 @@
 # PSMatch 1.15
 
+## PSMatch 1.17.1
+
+- Added parameter `z` in `plotSpectraPTM()` and set it to `1:precursorCharge(x)`
+  by default when it used to only display charge 1 before.
+
+## PSMatch 1.17.0
+
+- New Bioconductor devel.
+
 ## PSMatch 1.15.3
 
 - Adjusted documentation on `addCarbamidomethyl = TRUE` in
@@ -166,4 +175,4 @@
 
 ## Changes in 0.99.0
 
-- Prepare package for Bioconductor submission.
+- Prepare package for Bioconductor submission.

R/fragments-label.R

@@ -19,6 +19,11 @@
 ##'     whether labels should be fragment ions, , or their m/z values. If the
 ##'     latter, then the m/z values are named with the ion labels.
 ##'
+##' @param z `numeric()` or `list()`. Charge states passed to
+##'     [calculateFragments()]. A plain vector is applied uniformly to all
+##'     spectra; a list of the same length as `x` applies per-spectrum charge
+##'     states. Default is `1L`.
+##'
 ##' @param ... additional parameters (except `verbose`) passed to
 ##'     [calculateFragments()] to calculate fragment m/z values to be
 ##'     added to the spectra in `x`.
@@ -87,7 +92,7 @@
 ##' ## By default used in `plotSpectraPTM()`.
 ##' plotSpectraPTM(sp)
 labelFragments <- function(x, tolerance = 0, ppm = 20,
-                           what = c("ion", "mz"), ...) {
+                           what = c("ion", "mz"), z = 1L, ...) {
     stopifnot(requireNamespace("Spectra"))
     stopifnot(inherits(x, "Spectra"))
     what <- match.arg(what)
@@ -99,7 +104,8 @@ labelFragments <- function(x, tolerance = 0, ppm = 20,
         stopifnot("sequence" %in% Spectra::spectraVariables(x[j]))
         y <- Spectra::spectraData(x[j])[["sequence"]]
         x_data <- v[[j]]
-        y_data <- calculateFragments(y, verbose = FALSE, ...)
+        z_j <- if (is.list(z)) z[[j]] else z
+        y_data <- calculateFragments(y, verbose = FALSE, z = z_j, ...)
 
         y_data <- split(y_data, y_data$peptide)
 
@@ -129,4 +135,4 @@ labelFragments <- function(x, tolerance = 0, ppm = 20,
     super_labels <- unlist(super_labels, recursive = FALSE)
     attr(super_labels, "group") <- k
     super_labels
-}
+}

R/plotSpectra-PTM.R

@@ -82,14 +82,20 @@
 ##' details on this, see the appropriate vignette by running
 ##' `vignette("Fragments", package = "PSMatch")
 ##'
+##' @param z `numeric()` or `list()` passed to `calculateFragments()` via
+##'     `labelFragments()`. A plain vector is applied uniformly to all spectra;
+##'     a list of the same length as `x` applies per-spectrum charge states.
+##'     When `NULL` (default), each spectrum uses `1:precursorCharge` for that
+##'     spectrum, falling back to `1L` when the precursor charge is missing.
+##'
 ##' @param ... additional parameters to be passed to the `labelFragments()`
 ##'     and `calculateFragments()` functions.
 ##'
 ##' @importFrom graphics layout par
 ##'
 ##' @importFrom grDevices n2mfrow
 ##'
-##' @importFrom Spectra spectraVariables
+##' @importFrom Spectra spectraVariables precursorCharge
 ##'
 ##' @author Johannes Rainer, Sebastian Gibb, Guillaume Deflandre, Laurent Gatto
 ##'
@@ -172,6 +178,7 @@ plotSpectraPTM <- function(x, deltaMz = TRUE, ppm = 20,
                            fixedModifications = NULL,
                            variableModifications = NULL,
                            addCarbamidomethyl = TRUE,
+                           z = NULL,
                            ...) {
     if (!("sequence" %in% Spectra::spectraVariables(x))) {
         stop("Missing 'sequence' in Spectra::spectraVariables(x)")
@@ -196,21 +203,36 @@ plotSpectraPTM <- function(x, deltaMz = TRUE, ppm = 20,
                 xi
             })
         })
+        ## in case spectrum-specific charges states are given
+        if (is.list(z) && length(z) == length(x)) {
+            expansion_counts <- lengths(parts)
+            z <- rep(z, times = expansion_counts)
+        }
+
         x <- do.call(c, unlist(parts, recursive = FALSE))
     }
 
+    ## Build per-spectrum charge state list when z is not provided.
+    ## Done after modifications for correct length if variable mods used.
+    if (is.null(z)) {
+        charges <- Spectra::precursorCharge(x)
+        z <- lapply(charges, function(ch) {
+            if (!is.na(ch) && ch > 0L) seq_len(ch) else 1L
+        })
+    }
+
     nsp <- length(x)
     old_par <- par(no.readonly = TRUE)
     on.exit(par(old_par))
 
     if (length(main) != nsp) main <- rep(main[1], nsp)
 
     labels <- labelFragments(x, ppm = ppm, what = "ion",
-        addCarbamidomethyl = addCarbamidomethyl, ...)
+        addCarbamidomethyl = addCarbamidomethyl, z = z, ...)
 
     if (deltaMz) { ## Generate deltaMzData labels for .plot_single_spectrum_PTM
         deltaMzData <- labelFragments(x, ppm = ppm, what = "mz",
-            addCarbamidomethyl = addCarbamidomethyl, ...)
+            addCarbamidomethyl = addCarbamidomethyl, z = z, ...)
         layout_matrix <- .make_layout_matrix(length(labels))
         layout(layout_matrix,
                heights = rep(c(5, 1), length.out = nrow(layout_matrix)))
@@ -353,7 +375,7 @@ plotSpectraPTM <- function(x, deltaMz = TRUE, ppm = 20,
     .(basename(spectraData(x)[["dataOrigin"]])) *
     "/scan: " * .(spectraData(x)[["scanIndex"]]) *
     "/rt: " * .(round(spectraData(x)[["rtime"]], 2L)) *
-    "/charge: " * .(spectraData(x)[["charge"]]) *
+    "/charge: " * .(spectraData(x)[["precursorCharge"]]) *
     "/peptide: " * bold(.(peptide_sequence))
     )