{
  "_id": "6adfef375d0f7c3164ef698b",
  "Package": "lcmsPlot",
  "Type": "Package",
  "Title": "Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS)\ndata visualisation package",
  "Version": "1.1.21",
  "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'xcms-raw-list.R' 'raw-data.R' 'options.R' 'processing-xcms.R'\n'data-source.R' 'data-source-compound-discoverer.R'\n'data-source-mzmine.R' 'data-source-ms-dial.R'\n'data-source-compound-discoverer-node.R'\n'data-source-lipid-search.R' 'data-source-mztab.R'\n'data-validation.R' 'data-adapters.R'\n'lcmsPlotDataContainer-class.R' 'helpers-peaks.R'\n'raw-extract.R' 'dataset-chromatograms.R'\n'dataset-mass-traces.R' 'dataset-spectra.R'\n'dataset-intensity-map.R' 'dataset-total-ion-current.R'\n'dataset-rt-diff.R' 'dataset-peak-density.R'\n'dataset-peak-count-image.R' 'dataset-purity.R' 'plot-units.R'\n'plot-theme.R' 'plot-chrom-peak-rects.R' 'plot-chromatogram.R'\n'plot-mass-trace.R' 'plot-spectrum.R'\n'plot-total-ion-current.R' 'plot-intensity-map.R'\n'plot-peak-density.R' 'plot-peak-count-image.R'\n'plot-rt-diff.R' 'plot-purity.R' 'plot-variants.R' 'plot.R'\n'plot-data.R' 'lcmsPlot-class.R' 'layers-data.R'\n'layers-sources.R' 'layers-purity.R' 'layers-layout.R'\n'subset-features.R' 'app-utils.R' 'app-options.R'\n'app-module-chromatogram.R' 'app-module-peak-density.R'\n'app-module-spectra.R' 'app-module-tic.R' 'app-interface.R'\n'app-launcher.R'",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/computational-metabolomics/lcmsPlot",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "Metabolomics, MassSpectrometry",
  "BugReports": "https://github.com/computational-metabolomics/lcmsPlot/issues",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.1.1",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-26 12:06:24 UTC",
  "RemoteUrl": "https://github.com/bioc/lcmsPlot",
  "RemoteRef": "HEAD",
  "RemoteSha": "26fe7cd3348a5da367d1833182fab05527ccb012",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-26 23:31:04 UTC",
    "User": "root"
  },
  "Author": "Ossama Edbali [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0132-8668>),\nRalf Johannes Maria Weber [aut] (ORCID:\n<https://orcid.org/0000-0002-8796-4771>)",
  "Maintainer": "Ossama Edbali <o.edbali@bham.ac.uk>",
  "_user": "bioc",
  "_type": "src",
  "_file": "lcmsPlot_1.1.21.tar.gz",
  "_fileid": "https://r2.ropensci.org/71dade90d956b6a105345cb8038cb69c26030dd24d3629208eb1fb45360e33ae",
  "_filesize": 7706437,
  "_sha256": "71dade90d956b6a105345cb8038cb69c26030dd24d3629208eb1fb45360e33ae",
  "_expires": "2027-02-04T00:24:20.000Z",
  "_created": "2026-10-26T23:31:04.000Z",
  "_published": "2026-10-27T00:24:22.830Z",
  "_upstream": "https://github.com/bioc/lcmsPlot",
  "_status": "success",
  "_maintainer": {
    "name": "Ossama Edbali",
    "email": "o.edbali@bham.ac.uk",
    "login": "oss6",
    "orcid": "0000-0003-0132-8668",
    "description": "Experimental Officer in Computational Metabolomics at Phenome Centre Birmingham (University of Birmingham)",
    "uuid": 4907450
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    "author": "Ossama Edbali <ossedb@gmail.com>",
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    "time": 1793016384
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  "_homeurl": "https://github.com/computational-metabolomics/lcmsplot",
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  "_exports": [
    "chromatograms",
    "CompoundDiscovererNodeSource",
    "create_xcms_raw_list",
    "detectedPeaks",
    "get_XCMSnExp_object_example",
    "iterate_plot_batches",
    "lcmsPlot",
    "lcmsPlotApp",
    "lcmsPlotDataContainer",
    "LipidSearchSource",
    "lp_arrange",
    "lp_chrom_peak_rects",
    "lp_chromatogram",
    "lp_compound_discoverer",
    "lp_facets",
    "lp_get_plot",
    "lp_grid",
    "lp_intensity_map",
    "lp_isolation_window",
    "lp_labels",
    "lp_layout",
    "lp_legend",
    "lp_lipid_search",
    "lp_mass_trace",
    "lp_mztab",
    "lp_peak_count_image",
    "lp_peak_density",
    "lp_purity_distribution",
    "lp_purity_overlay",
    "lp_purity_timeline",
    "lp_rt_diff_plot",
    "lp_rt_line",
    "lp_spectra",
    "lp_theme",
    "lp_total_ion_current",
    "MsDialPeaksSource",
    "MZmineFeatureListsSource",
    "MzTabMSource",
    "next_plot",
    "sampleMetadata",
    "show",
    "spectra",
    "subset_features",
    "summaries",
    "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": "CompoundDiscovererNodeSource",
      "title": "Create a Compound Discoverer data source from a Scripting Node export",
      "topics": [
        "CompoundDiscovererNodeSource"
      ]
    },
    {
      "page": "CompoundDiscovererNodeSource-class",
      "title": "Compound Discoverer scripting-node data source",
      "topics": [
        "CompoundDiscovererNodeSource-class"
      ]
    },
    {
      "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": "lcmsPlotApp",
      "title": "Launch the lcmsPlot interactive Shiny app",
      "topics": [
        "lcmsPlotApp"
      ]
    },
    {
      "page": "lcmsPlotClass-class",
      "title": "Managing LC-MS data for visualisation",
      "topics": [
        "lcmsPlotClass-class"
      ]
    },
    {
      "page": "lcmsPlotDataContainer",
      "title": "Create an instance of class 'lcmsPlotDataContainer' from a data object",
      "topics": [
        "lcmsPlotDataContainer"
      ]
    },
    {
      "page": "lcmsPlotDataContainer-accessors",
      "title": "Access the data held by an 'lcmsPlotDataContainer'",
      "topics": [
        "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"
      ]
    },
    {
      "page": "lcmsPlotDataContainer-class",
      "title": "A unified storing mechanism for LC-MS data",
      "topics": [
        "lcmsPlotDataContainer-class"
      ]
    },
    {
      "page": "LipidSearchSource",
      "title": "Create a data source from a LipidSearch result file",
      "topics": [
        "LipidSearchSource"
      ]
    },
    {
      "page": "LipidSearchSource-class",
      "title": "LipidSearch data source",
      "topics": [
        "LipidSearchSource-class"
      ]
    },
    {
      "page": "lp_arrange",
      "title": "Define the arrangement of chromatograms",
      "topics": [
        "lp_arrange"
      ]
    },
    {
      "page": "lp_chrom_peak_rects",
      "title": "Plot chromatographic peak boundaries in the rt / m/z plane",
      "topics": [
        "lp_chrom_peak_rects"
      ]
    },
    {
      "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_isolation_window",
      "title": "Visualise the isolation window for a precursor fragmentation event",
      "topics": [
        "lp_isolation_window"
      ]
    },
    {
      "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_lipid_search",
      "title": "Define the options to use when plotting LC-MS data coming from a LipidSearch result file.",
      "topics": [
        "lp_lipid_search"
      ]
    },
    {
      "page": "lp_mass_trace",
      "title": "Define the mass trace to plot",
      "topics": [
        "lp_mass_trace"
      ]
    },
    {
      "page": "lp_mztab",
      "title": "Define the options to use when plotting LC-MS data coming from an mzTab-M file.",
      "topics": [
        "lp_mztab"
      ]
    },
    {
      "page": "lp_peak_count_image",
      "title": "Plot chromatographic peak counts per retention-time bin",
      "topics": [
        "lp_peak_count_image"
      ]
    },
    {
      "page": "lp_peak_density",
      "title": "Plot the peak density for one or more m/z features",
      "topics": [
        "lp_peak_density"
      ]
    },
    {
      "page": "lp_purity_distribution",
      "title": "Plot the distribution of precursor ion purity scores per sample",
      "topics": [
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    },
    {
      "page": "lp_purity_overlay",
      "title": "Overlay precursor ion purity scores on a chromatogram",
      "topics": [
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    },
    {
      "page": "lp_purity_timeline",
      "title": "Plot precursor ion purity scores as a timeline",
      "topics": [
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    {
      "page": "lp_rt_diff_plot",
      "title": "Generate the retention time difference plot between raw and adjusted datasets",
      "topics": [
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    },
    {
      "page": "lp_rt_line",
      "title": "Define a vertical line on a retention time value",
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    {
      "page": "lp_spectra",
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      "page": "lp_theme",
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      "page": "lp_total_ion_current",
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      "topics": [
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    {
      "page": "MsDialPeaksSource",
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      "topics": [
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    {
      "page": "MZmineFeatureListsSource",
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      "page": "MzTabMSource-class",
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      "page": "next_plot",
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    {
      "page": "show-CompoundDiscovererNodeSource-method",
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      "topics": [
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      "page": "show-ExternalDataSource-method",
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      "topics": [
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    {
      "page": "show-lcmsPlotClass-method",
      "title": "Plot the 'lcmsPlotClass' object",
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      "page": "show-LipidSearchSource-method",
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