Changes in version 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. Changes in version 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. Changes in version 0.99.16 - Fixed <- vs = assignment NOTE raised by R CMD CHECK. Changes in version 0.99.15 - Addressed second round of Bioconductor pre-acceptance review comments. Changes in version 0.99.14 - Added titles to all vignette code chunks for improved readability. Changes in version 0.99.13 - Added runnable \dontrun{} examples to MZmineFeatureListsSource and MsDialPeaksSource documentation. Changes in version 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. Changes in version 0.99.11 - Version bump. Changes in version 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. Changes in version 0.99.9 - Removed redundant example from lcmsPlotClass documentation. Changes in version 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. Changes in version 0.99.7 - Added figure dimension options (fig.height, fig.width) to vignette chunks for consistent rendered output. Changes in version 0.99.6 - Version bump; standardised @return documentation across all exported functions. Changes in version 0.99.5 - Added @return documentation to exported functions. - Fixed xcms namespace qualification in the test helper. Changes in version 0.99.4 - Fixed use of AnnotatedDataFrame (was incorrectly using NAnnotatedDataFrame in some code paths). Changes in version 0.99.3 - Fixed namespace qualification for xcms and patchwork calls. Changes in version 0.99.2 - Fixed MulticoreParam call in vignette. Changes in version 0.99.1 - Fixed BiocParallel namespace registration in vignette. Changes in version 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. Changes in version 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").