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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lcmsPlot_1.0.0.tgz(r-4.6-any)lcmsPlot_1.0.0.tgz(r-4.5-any)
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lcmsPlot_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lcmsPlot/json (API)

# 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-1.1.24(bioc 3.24)lcmsPlot-1.0.0(bioc 3.23)

metabolomics massspectrometry

5.81 score 4 stars 7 scripts 180 downloads 26 exports 141 dependencies

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

Target	Result	Time
bioc-checks	NOTE	177
linux-devel	OK	407
source / vignettes	OK	409
linux-release	OK	365
macos-release	OK	366
macos-oldrel	OK	291
windows-devel	OK	613
windows-release	OK	605
windows-oldrel	OK	612
wasm-release	OK	149

Exports:create_data_container_from_obj create_xcms_raw_list get_XCMSnExp_object_example iterate_plot_batches lcmsPlot lp_arrange lp_chromatogram lp_compound_discoverer lp_facets lp_get_plot lp_grid lp_intensity_map lp_labels lp_layout lp_legend lp_mass_trace lp_peak_density lp_rt_diff_plot lp_rt_line lp_spectra lp_total_ion_current MsDialPeaksSource MZmineFeatureListsSource next_plot show XcmsRawList

Dependencies:abind affy affyio AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bit bit64 blob bslib cachem cli clue cluster codetools cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dir.expiry doParallel dplyr evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gtable highr hms htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MALDIquant MASS MassSpecWavelet Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mime MsBackendMsp MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment mzID mzR ncdf4 openssl otel patchwork pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch PTMods purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 Rhdf5lib rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite vsn withr xcms xfun XML XVector yaml

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

Rendered fromlcms_data_plotting.Rmdusingknitr::rmarkdown

Last update: 2026-04-05
Started: 2025-07-03

Creating publication-ready LC-MS data plots

Installation | Load data | Overview of the data | Custom themes | Session Info

Rendered fromcreating_publication_ready_plots.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
lcmsPlot: Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package	lcmsPlot-package
Apply a function to an 'lcmsPlotClass' object using the infix '+' operator	+,lcmsPlotClass,function-method
Create an 'XcmsRawList' from raw LC-MS files	create_xcms_raw_list
External data source wrapper	ExternalDataSource-class
Get an 'XCMSnExp' example object from the 'faahKO' dataset	get_XCMSnExp_object_example
Iterate on the batches of plots	iterate_plot_batches iterate_plot_batches,lcmsPlotClass,function-method
Create an 'lcmsPlotClass' object	lcmsPlot
Managing LC-MS data for visualisation	lcmsPlotClass-class
A unified storing mechanism for LC-MS data	lcmsPlotDataContainer-class
Define the arrangement of chromatograms	lp_arrange
Define the chromatograms to plot	lp_chromatogram
Define the options to use when plotting LC-MS data coming from Compound Discoverer results.	lp_compound_discoverer
Define the plot's faceting	lp_facets
Get the underlying plot object.	lp_get_plot
Define a gridded plot	lp_grid
Define a 2D intensity map	lp_intensity_map
Define the labels of the plot	lp_labels
Define the plot layout	lp_layout
Define the legend layout	lp_legend
Define the mass trace to plot	lp_mass_trace
Plot the peak density for one or more m/z features	lp_peak_density
Generate the retention time difference plot between raw and adjusted datasets	lp_rt_diff_plot
Define a vertical line on a retention time value	lp_rt_line
Define the spectra to plot	lp_spectra
Define the total ion current (TIC)	lp_total_ion_current
Create an MS-DIAL data source from peak lists	MsDialPeaksSource
Create an MZmine data source from feature lists	MZmineFeatureListsSource
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' object	show,lcmsPlotClass-method
Show a summary of an instance of class 'lcmsPlotDataContainer'	show,lcmsPlotDataContainer-method
Show a summary of an 'XcmsRawList' object	show,XcmsRawList-method
Create an 'XcmsRawList' object	XcmsRawList
A list of 'xcmsRaw' objects representing multiple samples	XcmsRawList-class