{
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  "Type": "Package",
  "Title": "Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS)\ndata visualisation package",
  "Version": "1.1.3",
  "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' 'creators-purity.R'\n'constructors-chromatograms.R' 'constructors-spectra.R'\n'data-validation.R' 'data-adapters.R' 'plot-units.R'\n'plot-chromatogram.R' 'plot-mass-trace.R' 'plot-spectrum.R'\n'plot-total-ion-current.R' 'plot-intensity-map.R'\n'plot-peak-density.R' 'plot-rt-diff.R' 'plot-purity.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' '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'",
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  "URL": "https://github.com/computational-metabolomics/lcmsPlot",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "Metabolomics, MassSpectrometry",
  "BugReports": "https://github.com/computational-metabolomics/lcmsPlot/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-03 08:47:30 UTC",
  "RemoteUrl": "https://github.com/bioc/lcmsPlot",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 21:39:23 UTC",
    "User": "root"
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  "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>)",
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    "create_xcms_raw_list",
    "get_XCMSnExp_object_example",
    "iterate_plot_batches",
    "lcmsPlot",
    "lcmsPlotApp",
    "lp_arrange",
    "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_mass_trace",
    "lp_peak_density",
    "lp_purity_distribution",
    "lp_purity_overlay",
    "lp_purity_timeline",
    "lp_rt_diff_plot",
    "lp_rt_line",
    "lp_spectra",
    "lp_total_ion_current",
    "MsDialPeaksSource",
    "MZmineFeatureListsSource",
    "next_plot",
    "show",
    "XcmsRawList"
  ],
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    {
      "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": "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-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_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_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_purity_distribution",
      "title": "Plot the distribution of precursor ion purity scores per sample",
      "topics": [
        "lp_purity_distribution"
      ]
    },
    {
      "page": "lp_purity_overlay",
      "title": "Overlay precursor ion purity scores on a chromatogram",
      "topics": [
        "lp_purity_overlay"
      ]
    },
    {
      "page": "lp_purity_timeline",
      "title": "Plot precursor ion purity scores as a timeline",
      "topics": [
        "lp_purity_timeline"
      ]
    },
    {
      "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"
      ]
    }
  ],
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