# Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package

## Documentation for package ‘lcmsPlot’ version 1.1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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