NEWS

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lcmsPlot 1.1.3

• Redesigned lcmsPlotApp() as a Tailwind-based dashboard: sticky topbar, left navigation rail with a card-style file uploader and sample picker, and a content area with the plot in a card. The Tailwind CSS is precompiled and shipped under inst/www/lcmsPlot.css; no runtime network or Node dependency. Dev sources live in tools/tailwind/ (excluded from the installed package).
• Added a per-tab Options panel that exposes lp_facets(), lp_arrange(), lp_legend(), and lp_labels() directly from the UI. Users can now facet, group, reposition the legend, and add titles without writing R code.
• Dashboard CSS is now served via htmltools::htmlDependency() and the Tailwind content scan + safelist were hardened so utility classes referenced from R templates actually end up in the compiled stylesheet. The UI is now wrapped in shiny::bootstrapPage() so the hidden tabsetPanel switches correctly. Card corners reduced from rounded-2xl to rounded-md, sidebar gap bumped to gap-6, and the initial nav highlight is now set statically in markup.
• The Shiny uploader now accepts additional data-source types: Thermo .raw files (multi-file), Compound Discoverer .cdResult SQLite results (single file), serialised XCMSnExp / MsExperiment objects via .rds (single file), and saved workspaces containing one such object via .RData / .rda (single file). All existing mzML / CDF workflows are unchanged.

lcmsPlot 1.1.2

• Added lcmsPlotApp(), an interactive Shiny app for exploring raw LC-MS files. Users can upload one or more mzML / CDF files and view base-peak and total-ion chromatograms, extract ion chromatograms by m/z and ppm (with an optional retention-time window), inspect peak density across samples, and plot spectra by scan index. The app follows Bioconductor's Shiny code-organisation guidelines: all UI/server code lives in R/ and lcmsPlotApp() returns a shinyApp object rather than calling runApp() internally. shiny, shinytoastr, and shinytest2 were added to Suggests.

lcmsPlot 1.1.1

• Added support for purityA objects (msPurity) as the data_obj input to lcmsPlot(), enabling direct visualisation of precursor ion purity results.
• Added lp_purity_overlay(): overlays per-scan inPurity scores as coloured points on a chromatogram, with a diverging colour scale and an optional threshold midpoint.
• Added lp_purity_timeline(): scatter plot of inPurity versus retention time per sample, with an optional horizontal threshold line.
• Added lp_purity_distribution(): violin or boxplot distribution of inPurity scores grouped by sample, with an optional threshold line.
• Added lp_isolation_window(): MS1 spectrum plot annotated with the isolation window rectangle, precursor m/z dashed line, and inPurity score as a subtitle.
• Added purity_scores slot to lcmsPlotDataContainer for storing per-scan purity data extracted from purityA@puritydf.
• Added msPurity to Suggests in DESCRIPTION.

lcmsPlot 0.99.20

• Added lp_peak_density() for peak density plots that mirror xcms::plotChromPeakDensity(): y-axis shows sample indices positioned within the kernel density range, x-axis shows RT, coloured points mark individual detected peaks per sample, and a density line is overlaid. When min_fraction and sample_groups are provided the density-descent grouping algorithm is simulated and semi-transparent rectangles highlight RT regions that would form feature groups. When used after lp_chromatogram(), features is inherited automatically. Supports rt_unit ("second" / "minute"), bw, min_samples, max_features, and multiple m/z windows with auto-faceting.
• Fixed highlight_peaks_mode = "rectangle" and "point" in lp_chromatogram(): geoms now use inherit.aes = FALSE to avoid evaluating the global x = rt_plot aesthetic against detected_peaks, which previously caused an object 'rt_plot' not found error. RT values for rectangle and point modes are now scaled correctly when rt_unit = "minute".
• Added line_type parameter to lp_chromatogram() (passed through to geom_line(); any ggplot2 linetype string is accepted).
• Added x_dim, y_dim, and fill_scale parameters to lp_intensity_map(), allowing the m/z and RT axes to be swapped and the fill colour scale to be replaced with any ggplot2 scale object.
• Expanded the "Plot peak density" section of the lcms_data_plotting vignette with explanatory prose and a combined chromatogram + peak density example.

lcmsPlot 0.99.19

• Migrated all internal data structures from data.frame to tibble; tibble is now a formal Imports dependency.
• Fixed all_of() call in the DBIConnection chromatogram creator to pass column names as a single character vector.
• Qualified tibble() calls in MZmineFeatureListsSource and MsDialPeaksSource examples as tibble::tibble() to avoid could not find function "tibble" errors during R CMD check.
• Expanded get_metadata() documentation with dedicated sections describing the behaviour for all nine dispatch methods: character, XCMSnExp, MsExperiment, MChromatograms, XChromatograms, XChromatogram, XcmsRawList, ExternalDataSource, and DBIConnection.

lcmsPlot 0.99.18

• Added support for xcmsRaw objects via the new XcmsRawList S4 container and create_xcms_raw_list() convenience helper that reads files in parallel via BiocParallel.
• Added XcmsRawReader, a MsRawReader subclass that reads scan headers and peaks directly from in-memory xcmsRaw slots without opening a file connection.
• Added support for XChromatograms, XChromatogram, and MChromatograms as direct data inputs to lcmsPlot().
• XChromatograms now automatically derive a feature_id from the m/z and RT ranges of each row, enabling faceting and gridding on feature_id.
• Refactored the chromatogram creator into a unified create_chromatograms() S4 generic replacing the four previous specialised generics.
• Added na.rm argument to lp_chromatogram() to remove data points with NA intensity before plotting.
• Added GitHub Actions CI workflow (.github/workflows/R-CMD-check.yaml) that runs devtools::test() and rcmdcheck::rcmdcheck() against the Bioconductor devel Docker image on every push and pull request to devel.

lcmsPlot 0.99.16

• Fixed <- vs = assignment NOTE raised by R CMD CHECK.

lcmsPlot 0.99.15

• Addressed second round of Bioconductor pre-acceptance review comments.

lcmsPlot 0.99.14

• Added titles to all vignette code chunks for improved readability.

lcmsPlot 0.99.13

• Added runnable \dontrun{} examples to MZmineFeatureListsSource and MsDialPeaksSource documentation.

lcmsPlot 0.99.12

• Added support for MZmine (v2+) feature lists via MZmineFeatureListsSource.
• Added support for MS-DIAL peak tables via MsDialPeaksSource.
• Updated vignette with MZmine and MS-DIAL interoperability sections.

lcmsPlot 0.99.11

• Version bump.

lcmsPlot 0.99.10

• Added support for Compound Discoverer results files (.cdResult) via a new SQL-based data source backed by DBI / RSQLite.
• Added lp_compound_discoverer() for loading and querying Compound Discoverer results directly within the lcmsPlot pipeline.
• Updated lcmsPlot class documentation.

lcmsPlot 0.99.9

• Removed redundant example from lcmsPlotClass documentation.

lcmsPlot 0.99.8

• Major codebase refactoring for Bioconductor standards compliance.
• get_metadata() for XCMSnExp and MsExperiment now falls back to deriving sample_id from file basenames when no sample_id_column is present.

lcmsPlot 0.99.7

• Added figure dimension options (fig.height, fig.width) to vignette chunks for consistent rendered output.

lcmsPlot 0.99.6

• Version bump; standardised @return documentation across all exported functions.

lcmsPlot 0.99.5

• Added @return documentation to exported functions.
• Fixed xcms namespace qualification in the test helper.

lcmsPlot 0.99.4

• Fixed use of AnnotatedDataFrame (was incorrectly using NAnnotatedDataFrame in some code paths).

lcmsPlot 0.99.3

• Fixed namespace qualification for xcms and patchwork calls.

lcmsPlot 0.99.2

• Fixed MulticoreParam call in vignette.

lcmsPlot 0.99.1

• Fixed BiocParallel namespace registration in vignette.

lcmsPlot 0.99.0

• Initial Bioconductor submission.
• Added comprehensive roxygen2 documentation with examples for all exported functions.
• Added testthat (edition 3) test suite covering chromatogram, spectra, and intensity map creators.
• Updated README with package overview and usage example.

lcmsPlot 0.1.0

• Initial implementation of lcmsPlot.
• lcmsPlot() entry point accepting MsExperiment, XCMSnExp, and raw file paths (character) as data sources.
• lp_chromatogram(): base peak chromatograms (BPC), total ion chromatograms (TIC), and extracted ion chromatograms (XIC) with configurable m/z and RT tolerances.
• lp_spectra(): mass spectra extraction with "closest", "closest_apex", and "across_peak" scan-selection modes; standalone and chromatogram-linked display; spectral mirror plots.
• lp_intensity_map(): two-dimensional m/z vs RT intensity maps with optional density smoothing.
• lp_total_ion_current(): TIC distributions as violin or box plots.
• lp_mass_trace(): mass trace overlays below chromatogram panels.
• lp_rt_line(): vertical reference lines at specified retention times.
• lp_rt_diff_plot(): retention-time correction diagnostic plot.
• lp_facets(), lp_grid(), lp_arrange(), lp_layout(): flexible panel layout helpers.
• lp_labels(), lp_legend(): axis and legend annotation helpers.
• highlight_peaks and highlight_apices options in lp_chromatogram().
• MsExperiment support including retention-time corrected chromatograms (rt_type = "corrected" / "both").