Merge pull request #116 from rformassspectrometry/jomain

Add parameter scalePeaks to plotSpectraMirror

.github/workflows/check-bioc.yml

@@ -53,9 +53,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.19'}
-          - { os: windows-latest, r: 'devel', bioc: '3.19'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MetaboAnnotation
 Title: Utilities for Annotation of Metabolomics Data
-Version: 1.7.5
+Version: 1.9.1
 Description:
     High level functions to assist in annotation of (metabolomics) data sets.
     These include functions to perform simple tentative annotations based on

NAMESPACE

@@ -84,6 +84,8 @@ importFrom(S4Vectors,endoapply)
 importFrom(Spectra,MsBackendDataFrame)
 importFrom(Spectra,Spectra)
 importFrom(Spectra,joinPeaks)
+importFrom(Spectra,scalePeaks)
+importFrom(grDevices,n2mfrow)
 importFrom(graphics,par)
 importFrom(methods,"slot<-")
 importFrom(methods,as)

NEWS.md

@@ -1,3 +1,10 @@
+# MetaboAnnotation 1.9
+
+## Changes in 1.9.1
+
+- Add parameter `scalePeaks` to `plotSpectraMirror` to allow scaling peak
+  intensities before plotting.
+
 # MetaboAnnotation 1.7
 
 ## Changes in 1.7.5

R/MatchedSpectra.R

@@ -96,8 +96,10 @@
 #'
 #' - `plotSpectraMirror`: creates a mirror plot between the query and each
 #'   matching target spectrum. Can only be applied to a `MatchedSpectra` with a
-#'   single query spectrum. Additional plotting parameters can be passed through
-#'   `...`.
+#'   single query spectrum. Setting parameter `scalePeaks = TRUE` will scale
+#'   the peak intensities per spectrum to a total sum of one for a better
+#'   graphical visualization. Additional plotting parameters can be passed
+#'   through `...`.
 #'
 #' - `setBackend`: allows to change the *backend* of both the query and target
 #'   [Spectra()] object. The function will return a `MatchedSpectra` object with
@@ -123,6 +125,10 @@
 #'
 #' @param object `MatchedSpectra` object.
 #'
+#' @param scalePeaks for `plotSpectraMirror`: `logical(1)` if peak intensities
+#'   (per spectrum) should be scaled to a total sum of one (per spectrum) prior
+#'   to plotting.
+#'
 #' @param spectraVariables for `addProcessing`: `character` with additional
 #'   spectra variables that should be passed along to the function defined
 #'   with `FUN`. See [Spectra()] for details.
@@ -405,21 +411,29 @@ setMethod(
 #'
 #' @importFrom graphics par
 #'
+#' @importFrom grDevices n2mfrow
+#'
+#' @importFrom Spectra scalePeaks
+#'
 #' @export
-setMethod("plotSpectraMirror", "MatchedSpectra", function(x, xlab = "m/z",
-                                                          ylab = "intensity",
-                                                          main = "", ...) {
-    if (length(query(x)) != 1)
-        stop("Length of 'query(x)' has to be 1.")
-    y <- x@target[x@matches$target_idx]
-    if (!length(y))
-        y <- Spectra(DataFrame(msLevel = 2L))
-    nr <- sqrt(max(length(y), 1))
-    par(mfrow = c(floor(nr), ceiling(nr)))
-    for (i in seq_along(y))
-        plotSpectraMirror(x = query(x)[1L], y = y[i],
-                          xlab = xlab, ylab = ylab, main = main, ...)
-})
+setMethod(
+    "plotSpectraMirror", "MatchedSpectra",
+    function(x, xlab = "m/z", ylab = "intensity", main = "",
+             scalePeaks = FALSE, ...) {
+        if (length(query(x)) != 1)
+            stop("Length of 'query(x)' has to be 1.")
+        y <- x@target[x@matches$target_idx]
+        if (!length(y))
+            y <- Spectra(DataFrame(msLevel = 2L))
+        if (scalePeaks) {
+            x <- scalePeaks(query(x)[1L])
+            y <- scalePeaks(y)
+        } else x <- query(x)[1L]
+        par(mfrow = n2mfrow(length(y)))
+        for (i in seq_along(y))
+            plotSpectraMirror(x = x, y = y[i],
+                              xlab = xlab, ylab = ylab, main = main, ...)
+    })
 
 #' @importMethodsFrom ProtGenerics setBackend
 #'

tests/testthat/test_MatchedSpectra.R

@@ -220,6 +220,12 @@ test_that("pruneTarget,MatchedSpectra works", {
 test_that("plotSpectraMirror throws an error", {
     ms <- MatchedSpectra()
     expect_error(plotSpectraMirror(ms), "Length")
+
+    ms <- MatchedSpectra(sp1, sp2, matches = data.frame(query_idx = integer(),
+                                                        target_idx = integer(),
+                                                        score = numeric()))
+    plotSpectraMirror(ms[1])
+    plotSpectraMirror(ms[1], scalePeaks = TRUE)
 })
 
 test_that("addProcessing works", {