Package: lcmsPlot 1.0.0

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_1.0.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
lcmsPlot/json (API)
NEWS

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

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

On BioConductor:lcmsPlot-1.1.1(bioc 3.24)lcmsPlot-1.0.0(bioc 3.23)

metabolomicsmassspectrometry

5.53 score 1 stars 176 downloads 26 exports 141 dependencies

Last updated from:146cffe811 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

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bioc-checksNOTE230
linux-devel-x86_64OK401
source / vignettesOK415
linux-release-x86_64OK422
macos-release-arm64OK207
macos-oldrel-arm64OK250
windows-develOK755
windows-releaseOK616
windows-oldrelOK564
wasm-releaseOK218

Exports:create_data_container_from_objcreate_xcms_raw_listget_XCMSnExp_object_exampleiterate_plot_batcheslcmsPlotlp_arrangelp_chromatogramlp_compound_discovererlp_facetslp_get_plotlp_gridlp_intensity_maplp_labelslp_layoutlp_legendlp_mass_tracelp_peak_densitylp_rt_diff_plotlp_rt_linelp_spectralp_total_ion_currentMsDialPeaksSourceMZmineFeatureListsSourcenext_plotshowXcmsRawList

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbitbit64blobbslibcachemcliclueclustercodetoolscpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsBackendMspMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpatchworkpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

Creating publication-ready LC-MS data plots

Ossama Edbali

Rendered fromcreating_publication_ready_plots.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-01-04
Started: 2025-09-26

Easy-to-use, intuitive, and efficient LC-MS data plotting with lcmsPlot

Ossama Edbali

Rendered fromlcms_data_plotting.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-05
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 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
Managing LC-MS data for visualisationlcmsPlotClass-class
A unified storing mechanism for LC-MS datalcmsPlotDataContainer-class
Define the arrangement of chromatogramslp_arrange
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
Define the labels of the plotlp_labels
Define the plot layoutlp_layout
Define the legend layoutlp_legend
Define the mass trace to plotlp_mass_trace
Plot the peak density for one or more m/z featureslp_peak_density
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 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
Move to the next plot object (batch-mode)next_plot next_plot,lcmsPlotClass-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 an 'XcmsRawList' objectshow,XcmsRawList-method
Create an 'XcmsRawList' objectXcmsRawList
A list of 'xcmsRaw' objects representing multiple samplesXcmsRawList-class