{ "_id": "6a19563eacfb0bcc41de1ccf", "Package": "lcmsPlot", "Type": "Package", "Title": "Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS)\ndata visualisation package", "Version": "1.0.0", "Authors@R": "c(\nperson(\n\"Ossama\",\n\"Edbali\",\nrole=c(\"aut\",\"cre\"),\nemail=\"o.edbali@bham.ac.uk\",\ncomment = c(ORCID = \"0000-0003-0132-8668\")),\nperson(\nc(\"Ralf\",\"Johannes\", \"Maria\"),\n\"Weber\",\nrole=c(\"aut\"),\nemail=\"r.j.weber@bham.ac.uk\",\ncomment = c(ORCID = \"0000-0002-8796-4771\")))", "Description": "lcmsPlot is an R package designed for visualising Liquid\nChromatography-Mass Spectrometry (LC-MS) data with\npublication-ready high-quality plots. The package enables users\nto generate and customise chromatograms, mass traces, spectra,\nand more with fine-tuned aesthetics and annotation options.", "License": "GPL-3", "Encoding": "UTF-8", "Collate": "'lcmsPlot-package.R' 'zzz.R' 'helpers-data.R' 'helpers-s4.R'\n'raw-file-reader.R' 'xcms-raw-list.R' 'options.R'\n'processing-xcms.R' 'data-source.R'\n'data-source-compound-discoverer.R' 'data-source-mzmine.R'\n'data-source-ms-dial.R' 'constructors-chromatograms.R'\n'constructors-spectra.R' 'data-validation.R' 'data-adapters.R'\n'plot-units.R' 'plot-chromatogram.R' 'plot-mass-trace.R'\n'plot-spectrum.R' 'plot-total-ion-current.R'\n'plot-intensity-map.R' 'plot-peak-density.R' 'plot-rt-diff.R'\n'plot-variants.R' 'plot.R' 'lcmsPlotDataContainer-class.R'\n'creators-chromatograms.R' 'creators-intensity-map.R'\n'creators-peak-density.R' 'creators-rt-diff.R'\n'creators-spectra.R' 'creators-total-ion-current.R'\n'lcmsPlot-class.R'", "VignetteBuilder": "knitr", "URL": "https://github.com/computational-metabolomics/lcmsPlot", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "biocViews": "Metabolomics, MassSpectrometry", "BugReports": "https://github.com/computational-metabolomics/lcmsPlot/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:06:23 UTC", "RemoteUrl": "https://github.com/bioc/lcmsPlot", "RemoteRef": "RELEASE_3_23", "RemoteSha": "146cffe811c30b16e27313cb9000d19bfd14ae83", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:48:00 UTC", "User": "root" }, "Author": "Ossama Edbali [aut, cre] (ORCID:\n),\nRalf Johannes Maria Weber [aut] (ORCID:\n)", "Maintainer": "Ossama Edbali ", "MD5sum": "8e54c17b74155e925b58cd34a72aaa05", "_user": "bioc-release", "_type": "src", "_file": "lcmsPlot_1.0.0.tar.gz", "_fileid": "3f5cc9bac0d924c553d7cf499993595799fcb1555d726f64431b49f83fa5c4b7", "_filesize": 4716742, "_sha256": "3f5cc9bac0d924c553d7cf499993595799fcb1555d726f64431b49f83fa5c4b7", "_created": "2026-05-29T07:48:00.000Z", "_published": "2026-05-29T09:02:54.378Z", "_jobs": [ { "job": 78459942231, "time": 230, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7285805868" }, { "job": 78459942217, "time": 401, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7285854461" }, { "job": 78459942257, "time": 422, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7285860074" }, { "job": 78459942234, "time": 250, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7287036654" }, { "job": 78459942250, "time": 207, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7287023271" }, { "job": 78459001303, "time": 415, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285738188" }, { "job": 78459942223, "time": 218, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285802134" }, { "job": 78459942269, "time": 755, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7285952823" }, { "job": 78459942263, "time": 564, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7285900450" }, { "job": 78459942254, "time": 616, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7285914143" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/lcmsPlot", "_commit": { "id": "146cffe811c30b16e27313cb9000d19bfd14ae83", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381583 }, "_maintainer": { "name": "Ossama Edbali", "email": "o.edbali@bham.ac.uk", "login": "oss6", "description": "Experimental Officer in Computational Metabolomics at Phenome Centre Birmingham (University of Birmingham)", "uuid": 4907450, "orcid": "0000-0003-0132-8668" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "MSnbase", "role": "Imports" }, { "package": "xcms", "role": "Imports" }, { "package": "MsExperiment", "role": "Imports" }, { "package": "mzR", "role": "Imports" }, { "package": "Spectra", "role": "Imports" }, { "package": "MsBackendMsp", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "openxlsx", "role": "Suggests" }, { "package": "faahKO", "role": "Suggests" }, { "package": "rawrr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 6 }, { "week": "2025-27", "n": 2 }, { "week": "2025-28", "n": 2 }, { "week": "2025-30", "n": 1 }, { "week": "2025-32", "n": 1 }, { "week": "2025-38", "n": 1 }, { "week": "2025-39", "n": 8 }, { "week": "2025-41", "n": 8 }, { "week": "2025-43", "n": 1 }, { "week": "2025-52", "n": 3 }, { "week": "2026-01", "n": 5 }, { "week": "2026-06", "n": 2 }, { "week": "2026-10", "n": 1 }, { "week": "2026-11", "n": 2 }, { "week": "2026-14", "n": 4 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.1", "bioc": "3.24" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "metabolomics", "massspectrometry" ], "_stars": 1, "_contributors": [ { "user": "oss6", "count": 62, "uuid": 4907450 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "rjmw", "count": 1, "uuid": 7114586 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 176, "source": "https://www.bioconductor.org/packages/stats/bioc/lcmsPlot" }, "_devurl": "https://github.com/computational-metabolomics/lcmsplot", "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/lcmsPlot.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/computational-metabolomics/lcmsplot", "_realowner": "bioc", "_cranurl": false, "_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" ], "_help": [ { "page": "lcmsPlot-package", "title": "lcmsPlot: Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package", "topics": [ "lcmsPlot-package" ] }, { "page": "plus-lcmsPlotClass-function-method", "title": "Apply a function to an 'lcmsPlotClass' object using the infix '+' operator", "topics": [ "+,lcmsPlotClass,function-method" ] }, { "page": "create_xcms_raw_list", "title": "Create an 'XcmsRawList' from raw LC-MS files", "topics": [ "create_xcms_raw_list" ] }, { "page": "ExternalDataSource-class", "title": "External data source wrapper", "topics": [ "ExternalDataSource-class" ] }, { "page": "get_XCMSnExp_object_example", "title": "Get an 'XCMSnExp' example object from the 'faahKO' dataset", "topics": [ "get_XCMSnExp_object_example" ] }, { "page": "iterate_plot_batches", "title": "Iterate on the batches of plots", "topics": [ "iterate_plot_batches", "iterate_plot_batches,lcmsPlotClass,function-method" ] }, { "page": "lcmsPlot", "title": "Create an 'lcmsPlotClass' object", "topics": [ "lcmsPlot" ] }, { "page": "lcmsPlotClass-class", "title": "Managing LC-MS data for visualisation", "topics": [ "lcmsPlotClass-class" ] }, { "page": "lcmsPlotDataContainer-class", "title": "A unified storing mechanism for LC-MS data", "topics": [ "lcmsPlotDataContainer-class" ] }, { "page": "lp_arrange", "title": "Define the arrangement of chromatograms", "topics": [ "lp_arrange" ] }, { "page": "lp_chromatogram", "title": "Define the chromatograms to plot", "topics": [ "lp_chromatogram" ] }, { "page": "lp_compound_discoverer", "title": "Define the options to use when plotting LC-MS data coming from Compound Discoverer results.", "topics": [ "lp_compound_discoverer" ] }, { "page": "lp_facets", "title": "Define the plot's faceting", "topics": [ "lp_facets" ] }, { "page": "lp_get_plot", "title": "Get the underlying plot object.", "topics": [ "lp_get_plot" ] }, { "page": "lp_grid", "title": "Define a gridded plot", "topics": [ "lp_grid" ] }, { "page": "lp_intensity_map", "title": "Define a 2D intensity map", "topics": [ "lp_intensity_map" ] }, { "page": "lp_labels", "title": "Define the labels of the plot", "topics": [ "lp_labels" ] }, { "page": "lp_layout", "title": "Define the plot layout", "topics": [ "lp_layout" ] }, { "page": "lp_legend", "title": "Define the legend layout", "topics": [ "lp_legend" ] }, { "page": "lp_mass_trace", "title": "Define the mass trace to plot", "topics": [ "lp_mass_trace" ] }, { "page": "lp_peak_density", "title": "Plot the peak density for one or more m/z features", "topics": [ "lp_peak_density" ] }, { "page": "lp_rt_diff_plot", "title": "Generate the retention time difference plot between raw and adjusted datasets", "topics": [ "lp_rt_diff_plot" ] }, { "page": "lp_rt_line", "title": "Define a vertical line on a retention time value", "topics": [ "lp_rt_line" ] }, { "page": "lp_spectra", "title": "Define the spectra to plot", "topics": [ "lp_spectra" ] }, { "page": "lp_total_ion_current", "title": "Define the total ion current (TIC)", "topics": [ "lp_total_ion_current" ] }, { "page": "MsDialPeaksSource", "title": "Create an MS-DIAL data source from peak lists", "topics": [ "MsDialPeaksSource" ] }, { "page": "MZmineFeatureListsSource", "title": "Create an MZmine data source from feature lists", "topics": [ "MZmineFeatureListsSource" ] }, { "page": "next_plot", "title": "Move to the next plot object (batch-mode)", "topics": [ "next_plot", "next_plot,lcmsPlotClass-method" ] }, { "page": "show-ExternalDataSource-method", "title": "Show a summary of an instance of class 'ExternalDataSource'", "topics": [ "show,ExternalDataSource-method" ] }, { "page": "show-lcmsPlotClass-method", "title": "Plot the 'lcmsPlotClass' object", "topics": [ "show,lcmsPlotClass-method" ] }, { "page": "show-lcmsPlotDataContainer-method", "title": "Show a summary of an instance of class 'lcmsPlotDataContainer'", "topics": [ "show,lcmsPlotDataContainer-method" ] }, { "page": "show-XcmsRawList-method", "title": "Show a summary of an 'XcmsRawList' object", "topics": [ "show,XcmsRawList-method" ] }, { "page": "XcmsRawList", "title": "Create an 'XcmsRawList' object", "topics": [ "XcmsRawList" ] }, { "page": "XcmsRawList-class", "title": "A list of 'xcmsRaw' objects representing multiple samples", "topics": [ "XcmsRawList-class" ] } ], "_readme": "https://github.com/bioc/lcmsPlot/raw/RELEASE_3_23/README.md", "_rundeps": [ "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" ], "_vignettes": [ { "source": "creating_publication_ready_plots.Rmd", "filename": "creating_publication_ready_plots.html", "title": "Creating publication-ready LC-MS data plots", "author": "Ossama Edbali", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Load data", "Overview of the data", "Custom themes", "Session Info" ], "created": "2025-09-26 10:58:49", "modified": "2026-01-04 12:53:39", "commits": 6 }, { "source": "lcms_data_plotting.Rmd", "filename": "lcms_data_plotting.html", "title": "Easy-to-use, intuitive, and efficient LC-MS data plotting with lcmsPlot", "author": "Ossama Edbali", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Objectives", "Installation", "Load data", "Samples summary", "The entry point to plot", "Plot base peak chromatogram (BPC)", "Plot total ion chromatogram (TIC)", "Total ion current", "Intensity maps", "Plot chromatograms", "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", "Plot standalone spectra", "Interoperability", "Compound Discoverer", "MZmine", "MS-DIAL", "Session Info" ], "created": "2025-07-03 11:35:34", "modified": "2026-04-05 15:20:08", "commits": 20 } ], "_score": 5.531478917042255, "_indexed": false, "_nocasepkg": "lcmsplot", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/lcmsPlot", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-29T07:52:01.000Z", "distro": "noble", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "24962346b6c6c036361d14f11c053cdddddbd1416328d816a923f7228c810545", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-29T07:52:28.000Z", "distro": "noble", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "01bab96b2cf9e70058bf8f3ea07b9c3dc197490f7f78752fc48fae80f69ecb1c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-29T09:00:11.000Z", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "fc4447585e9d7093f185267bf949e7e5750a407167241043f6a342301edcfcc8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-29T08:59:56.000Z", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "05685b8cb6fa36240e0b469310af470ead88254afd1d60f146552ba17ba6fb73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-29T07:52:02.000Z", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "dfff180218f2ef40455c46a5217c65b90ec7a647abec13f377f44d5d6057872c", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-29T07:52:24.000Z", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "137e05ab8f7b65cf00a0f84bf58e199cf6daf6d8c853d3b9afbf0c919e8db381", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-29T07:50:33.000Z", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "3568e0939bb903870876987405c2490ab03dbe75bc9412b49c6efafffa6aa220", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-29T07:50:40.000Z", "commit": "146cffe811c30b16e27313cb9000d19bfd14ae83", "fileid": "bb99c276600a3a494fc6161151994eecfcf87630f37f2689fd713e00391070b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624830357" } ] }