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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").
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