Package: lcmsPlot 1.1.21

Ossama Edbali

lcmsPlot: Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package

lcmsPlot is an R package designed for visualising Liquid Chromatography-Mass Spectrometry (LC-MS) data with publication-ready high-quality plots. The package enables users to generate and customise chromatograms, mass traces, spectra, and more with fine-tuned aesthetics and annotation options.

Authors:Ossama Edbali [aut, cre], Ralf Johannes Maria Weber [aut]

lcmsPlot_1.1.21.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lcmsPlot/json (API)

# Install 'lcmsPlot' in R:
install.packages('lcmsPlot', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/computational-metabolomics/lcmsplot/issues

On BioConductor:lcmsPlot-1.1.17(bioc 3.24)lcmsPlot-1.0.0(bioc 3.23)

metabolomicsmassspectrometry

6.20 score 4 stars 7 scripts 183 downloads 45 exports 142 dependencies

Last updated from:26fe7cd334. Checks:1 WARNING, 7 OK, 2 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING211
linux-develOK784
source / vignettesOK565
linux-releaseOK786
macos-releaseERROR739
macos-oldrelERROR777
windows-develOK2836
windows-releaseOK3110
windows-oldrelOK2584
wasm-releaseOK169

Exports:chromatogramsCompoundDiscovererNodeSourcecreate_xcms_raw_listdetectedPeaksget_XCMSnExp_object_exampleiterate_plot_batcheslcmsPlotlcmsPlotApplcmsPlotDataContainerLipidSearchSourcelp_arrangelp_chrom_peak_rectslp_chromatogramlp_compound_discovererlp_facetslp_get_plotlp_gridlp_intensity_maplp_isolation_windowlp_labelslp_layoutlp_legendlp_lipid_searchlp_mass_tracelp_mztablp_peak_count_imagelp_peak_densitylp_purity_distributionlp_purity_overlaylp_purity_timelinelp_rt_diff_plotlp_rt_linelp_spectralp_themelp_total_ion_currentMsDialPeaksSourceMZmineFeatureListsSourceMzTabMSourcenext_plotsampleMetadatashowspectrasubset_featuressummariesXcmsRawList

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbitbit64blobbslibcachemChromatogramscliclueclustercodetoolscpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsBackendMspMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpatchworkpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

Creating publication-ready LC-MS data plots
Installation | Load data | Overview of the data | Theme and palette presets | Custom themes | Session Info
Rendered fromcreating_publication_ready_plots.Rmdusingknitr::rmarkdown

Last update: 2026-10-26
Started: 2025-09-26

Easy-to-use, intuitive, and efficient LC-MS data plotting with lcmsPlot
Introduction | Objectives | Installation | Load data | Samples summary | The entry point to plot | Plot base peak chromatogram (BPC) | Plot total ion chromatogram (TIC) | Plot averaged ion chromatogram (AIC) | Total ion current | Intensity maps | Plot chromatograms | Quality control of peak detection | Chromatographic peak counts across the run | Peak boundaries in the m/z and retention time plane | Plot retention time alignment effect | Plot grouped peaks across samples (features) | Plot peak density alongside chromatograms | Plot chromatograms with mass traces | Plot chromatograms from raw files | Plot spectra | Select closest scan to a specified RT | Select scan closest to a detected peak apex | Select multiple scans across a detected peak | Select the MS2 spectra of a feature by precursor | Plot standalone spectra | Interoperability | Compound Discoverer | Compound Discoverer scripting node | MZmine | MS-DIAL | LipidSearch | mzTab-M | Session Info
Rendered fromlcms_data_plotting.Rmdusingknitr::rmarkdown

Last update: 2026-10-26
Started: 2025-07-03

Readme and manuals

Help Manual

Help pageTopics
lcmsPlot: Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation packagelcmsPlot-package
Apply a function to an 'lcmsPlotClass' object using the infix '+' operator+,lcmsPlotClass,function-method
Create a Compound Discoverer data source from a Scripting Node exportCompoundDiscovererNodeSource
Compound Discoverer scripting-node data sourceCompoundDiscovererNodeSource-class
Create an 'XcmsRawList' from raw LC-MS filescreate_xcms_raw_list
External data source wrapperExternalDataSource-class
Get an 'XCMSnExp' example object from the 'faahKO' datasetget_XCMSnExp_object_example
Iterate on the batches of plotsiterate_plot_batches iterate_plot_batches,lcmsPlotClass,function-method
Create an 'lcmsPlotClass' objectlcmsPlot
Launch the lcmsPlot interactive Shiny applcmsPlotApp
Managing LC-MS data for visualisationlcmsPlotClass-class
Create an instance of class 'lcmsPlotDataContainer' from a data objectlcmsPlotDataContainer
Access the data held by an 'lcmsPlotDataContainer'chromatograms,lcmsPlotClass-method chromatograms,lcmsPlotDataContainer-method detectedPeaks detectedPeaks,lcmsPlotClass-method detectedPeaks,lcmsPlotDataContainer-method lcmsPlotDataContainer-accessors sampleMetadata sampleMetadata,lcmsPlotClass-method sampleMetadata,lcmsPlotDataContainer-method spectra,lcmsPlotClass-method spectra,lcmsPlotDataContainer-method summaries summaries,lcmsPlotClass-method summaries,lcmsPlotDataContainer-method
A unified storing mechanism for LC-MS datalcmsPlotDataContainer-class
Create a data source from a LipidSearch result fileLipidSearchSource
LipidSearch data sourceLipidSearchSource-class
Define the arrangement of chromatogramslp_arrange
Plot chromatographic peak boundaries in the rt / m/z planelp_chrom_peak_rects
Define the chromatograms to plotlp_chromatogram
Define the options to use when plotting LC-MS data coming from Compound Discoverer results.lp_compound_discoverer
Define the plot's facetinglp_facets
Get the underlying plot object.lp_get_plot
Define a gridded plotlp_grid
Define a 2D intensity maplp_intensity_map
Visualise the isolation window for a precursor fragmentation eventlp_isolation_window
Define the labels of the plotlp_labels
Define the plot layoutlp_layout
Define the legend layoutlp_legend
Define the options to use when plotting LC-MS data coming from a LipidSearch result file.lp_lipid_search
Define the mass trace to plotlp_mass_trace
Define the options to use when plotting LC-MS data coming from an mzTab-M file.lp_mztab
Plot chromatographic peak counts per retention-time binlp_peak_count_image
Plot the peak density for one or more m/z featureslp_peak_density
Plot the distribution of precursor ion purity scores per samplelp_purity_distribution
Overlay precursor ion purity scores on a chromatogramlp_purity_overlay
Plot precursor ion purity scores as a timelinelp_purity_timeline
Generate the retention time difference plot between raw and adjusted datasetslp_rt_diff_plot
Define a vertical line on a retention time valuelp_rt_line
Define the spectra to plotlp_spectra
Define the theme and colour palette of the plotlp_theme
Define the total ion current (TIC)lp_total_ion_current
Create an MS-DIAL data source from peak listsMsDialPeaksSource
Create an MZmine data source from feature listsMZmineFeatureListsSource
Create a data source from an mzTab-M fileMzTabMSource
mzTab-M data sourceMzTabMSource-class
Move to the next plot object (batch-mode)next_plot next_plot,lcmsPlotClass-method
Show a summary of a 'CompoundDiscovererNodeSource' objectshow,CompoundDiscovererNodeSource-method
Show a summary of an instance of class 'ExternalDataSource'show,ExternalDataSource-method
Plot the 'lcmsPlotClass' objectshow,lcmsPlotClass-method
Show a summary of an instance of class 'lcmsPlotDataContainer'show,lcmsPlotDataContainer-method
Show a summary of a 'LipidSearchSource' objectshow,LipidSearchSource-method
Show a summary of a 'MzTabMSource' objectshow,MzTabMSource-method
Show a summary of an 'XcmsRawList' objectshow,XcmsRawList-method
Keep the data matching a condition on its annotationssubset_features
Create an 'XcmsRawList' objectXcmsRawList
A list of 'xcmsRaw' objects representing multiple samplesXcmsRawList-class