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feat: add support for Chromatograms to chromatogram #837

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Merged
sneumann merged 10 commits into from
Aug 17, 2026
Merged

feat: add support for Chromatograms to chromatogram #837

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c874427
feat: add support for Chromatograms to chromatogram
jorainer Jul 22, 2026
50e63ea
feat: add support for Chromatograms to chromPeakChromatograms
jorainer Jul 23, 2026
93a5438
feat: add support for Chromatograms to featureChromatograms
jorainer Jul 27, 2026
2920208
fix: chrom_data_for_ranges to properly replicate dataOrigin
jorainer Jul 27, 2026
b768b52
feat: add Chromatograms support for XcmsExperimentHdf5
jorainer Jul 28, 2026
c8cdb25
fix: loadXcmsData() updates processHistory
jorainer Aug 4, 2026
f4b04e6
fix: chromPeakData<- for XcmsExperiment supports DataFrame
jorainer Aug 6, 2026
7c97912
refactor: export XcmsExperimentHdf5 empty constructor
jorainer Aug 7, 2026
9996fe2
fix: avoid clash of multiple method definitions
jorainer Aug 7, 2026
fed19bc
refactor: import group generic from BiocGenerics
jorainer Aug 13, 2026
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3 changes: 2 additions & 1 deletion .github/workflows/check-bioc.yml
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Expand Up @@ -159,10 +159,11 @@ jobs:
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
install.packages("remotes")
BiocManager::install("RforMassSpectrometry/Chromatograms")
install.packages("pak")
pak::local_install_dev_deps(ask = FALSE)
pak::local_install(depdendencies = TRUE)
BiocManager::install(c("rmarkdown", "BiocStyle"))
continue-on-error: true
shell: Rscript {0}

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9 changes: 5 additions & 4 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
Package: xcms
Version: 4.11.1
Version: 4.11.2
Title: LC-MS and GC-MS Data Analysis
Description: Framework for processing and visualization of chromatographically
separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
Expand Down Expand Up @@ -53,7 +53,7 @@ Imports:
mzR (>= 2.25.3),
methods,
Biobase,
BiocGenerics,
BiocGenerics (>= 0.59.12),
ProtGenerics (>= 1.37.1),
lattice,
MassSpecWavelet (>= 1.66.0),
Expand All @@ -67,7 +67,8 @@ Imports:
progress,
RColorBrewer,
MetaboCoreUtils (>= 1.11.2),
data.table
data.table,
Chromatograms (>= 1.3.3)

@sneumann sneumann Aug 16, 2026

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BioC devel currently has Chromatograms 1.3.2, but the PR works if installed from GH.

Suggests:
BiocStyle,
caTools,
Expand All @@ -94,7 +95,6 @@ URL: https://github.com/sneumann/xcms
BugReports: https://github.com/sneumann/xcms/issues/new
VignetteBuilder: knitr
biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
RoxygenNote: 7.3.3
Encoding: UTF-8
Roxygen: list(markdown=TRUE)
Collate:
Expand Down Expand Up @@ -164,3 +164,4 @@ Collate:
'writemztab.R'
'xcmsSource.R'
'zzz.R'
Config/roxygen2/version: 8.1.0
16 changes: 12 additions & 4 deletions NAMESPACE
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Expand Up @@ -8,8 +8,8 @@ importMethodsFrom("ProtGenerics", "peaks", "chromatogram", "writeMSData",
"estimatePrecursorIntensity")
importClassesFrom("ProtGenerics", "Param")
importFrom("BiocGenerics", "updateObject", "fileName", "subset",
"dirname", "dirname<-")
## import("Biobase")
"dirname", "dirname<-")
importMethodsFrom("BiocGenerics", "group")
importFrom("Biobase", "AnnotatedDataFrame")
importClassesFrom("Biobase", "AnnotatedDataFrame")
importMethodsFrom("Biobase", "phenoData",
Expand Down Expand Up @@ -375,7 +375,6 @@ exportMethods("hasChromPeaks",
"removeIntensity",
"filterColumnsIntensityAbove",
"filterColumnsKeepTop",
"plotChromatogramsOverlay",
"transformIntensity",
"filterChromPeaks",
"filterFeatureDefinitions",
Expand All @@ -385,7 +384,9 @@ exportMethods("hasChromPeaks",
"chromPeakSpectra",
"chromPeakChromatograms",
"featureChromatograms",
"chromPeakSummary"
"chromPeakSummary",
"featureChromPeaks",
"featurePeakidx"
)

## feature grouping functions and methods.
Expand Down Expand Up @@ -467,3 +468,10 @@ export("BlankFlag")

## HDF5 storage mode
exportClasses("XcmsExperimentHdf5")
export("XcmsExperimentHdf5")

## Chromatograms
importMethodsFrom("Chromatograms", "Chromatograms")
importClassesFrom("Chromatograms", "Chromatograms")
importMethodsFrom("Chromatograms", "plotChromatogramsOverlay")
exportMethods("plotChromatogramsOverlay")
16 changes: 16 additions & 0 deletions NEWS.md
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@@ -1,5 +1,21 @@
# xcms 4.11

## Changes in version 4.11.2

- Add support to return chromatographic data as a `Chromatograms` object with
the `chromatogram()` method from `MsExperiment`, `XcmsExperiment` and
`XcmsExperimentHdf5` objects.
- Add support for `Chromatograms` to the `chromPeakChromatograms()` method for
`XcmsExperiment` and `XcmsExperimentHdf5` objects.
- Add support for `Chromatograms` to the `featureChromatograms()` method for
`XcmsExperiment` and `XcmsExperimentHdf5` objects.
- Add new methods `featureChromPeaks()` and `featurePeakidx()` to access the
mapping between features and chromatographic peaks.
- `loadXcmsData()` updates parameter class definitions in the object's *process
history*.
- Fix `chromPeakData<-` for `XcmsExperiment` not supporting a `DataFrame` as
input (issue #839).

## Changes in version 4.11.1

- `refineChromPeaks,MergeNeighboringPeakParam`: drop row names of intermediate
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