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Changelog

Source: NEWS.md

Changes in v0.99.10 (commit: ca9fab6)

Bug Fixes

  • pass release notes to prepare-news.sh for NEWS.md entries (c46971c)

Changes in v0.99.9 (commit: 50be182)

Features

  • Add include_columns parameter to gplot() for XChromatograms and MChromatograms, enabling plotly tooltip support with sample metadata. Accepts TRUE (all pData columns) or a character vector of specific column names.

Changes in v0.99.8 (commit: f36a3b1)

Features

  • Add color mapping by pData columns in gplot() for XChromatograms and MChromatograms. The col, peakCol, and peakBg parameters now accept either a static color string or a column name from Biobase::pData() for data-driven coloring.

Bug Fixes

  • Use default static colors in XCMS comparison plots in step3 vignette for visual parity with original XCMS output.

Changes in v0.99.7 (commit: f61c790)

Refactoring

  • Replace deprecated msdata with MsDataHub for test data loading (Johannes Rainer).
  • Reduce code duplication in gplot() for XChromatograms/XChromatogram (Johannes Rainer).
  • Call internal functions from xcms with ::: instead of reimplementing them (Johannes Rainer).
  • Enable examples and cosmetic source code improvements (Johannes Rainer).
  • Update and expand unit tests (Johannes Rainer).

Bug Fixes

  • Update pkgdown navbar links to match renamed vignettes.

Changes in v0.99.6

  • Load test data from MsDataHub dropping dependency from the deprecated msdata package (Johannes Rainer).
  • Reduce code duplication in gplot,XChromatograms/gplot,XChromatogram functions (Johannes Rainer).

Changes in v0.99.20

Bug Fixes

  • Add namespace prefix to .PROCSTEP.RTIME.CORRECTION (bbd8012)

Changes in v0.99.19

Bug Fixes

  • Add namespace prefix to .PROCSTEP.RTIME.CORRECTION in vignette (e4cf104)

Changes in v0.99.18

Bug Fixes

  • Update alignment-parameters vignette to avoid LamaParama validation error (9498619)
  • Update alignment-parameters vignette to eval and add XCMS comparison (094989e)
  • Update precursor-ions vignette with side-by-side comparison (27be196)

Features

  • Add gplot for LamaParama and gplotPrecursorIons (0a99b75)

Changes in v0.99.17

Bug Fixes

  • Resolve R CMD check warnings and errors (8327a96)

Changes in v0.99.16

Bug Fixes

  • add ‘Feature Group:’ label to tooltip text (13e2f84)
  • add text aesthetic to show Feature Group in plotly tooltips (4b94020)

Features

  • improve tooltips and vignette clarity for feature groups (bf6d4f8)

Changes in v0.99.15

Bug Fixes

  • properly separate line connections between feature groups (876b706)
  • resolve gplotFeatureGroups example errors and warnings (dbf8106)
  • sort features by m/z and limit vignette comparison plots (7105e7f)
  • use geom_path instead of geom_line to preserve m/z ordering (f2d8f23)

Features

  • Implement gplotFeatureGroups for feature group visualization (75f7a9e)

Changes in v0.99.14

Bug Fixes

  • add missing geom_vline import to gplotChromPeakDensity (405865a)
  • apply filterRt polygon fix to XChromatogram method (92c19ac)
  • completely rewrite gplotChromatogramsOverlay to match XCMS behavior (2faec0a)
  • correct layer ordering in gplotChromPeakDensity lower panel (bec5673)
  • correct rectangle positioning in gplotChromPeakDensity (7479e45)
  • correct stacking behavior in gplotChromatogramsOverlay (9194f79)
  • doc: formatting that makes rstudio live view happy (a83ef91)
  • handle infinite values in gplot polygon rendering (c8da796)
  • use Bootstrap grid instead of CSS flexbox for pkgdown compatibility (f79605d)
  • use filterRt() for polygon rendering to match XCMS exactly (1a5cb2a)
  • use patchwork & operator in vignette custom_ggplot example (dce3edc)

Features

  • add gplot() method for XcmsExperiment and XCMSnExp (8fd87fb)
  • add side-by-side comparison for correspondence results (b0113ad)
  • implement gplotChromatogramsOverlay for XChromatograms/MChromatograms (acfe633)
  • implement gplotChromPeakDensity for XChromatograms/MChromatograms (beff00d)

BREAKING CHANGES

  • gplotChromatogramsOverlay now correctly overlays multiple EICs (rows) from the same sample (column), not multiple samples across the same EIC. This matches the original XCMS behavior.

Changes in v0.99.13

Bug Fixes

  • correct pkgdown deployment and documentation link (a8f45ea)

Changes in v0.99.12

Bug Fixes

  • re-add .nojekyll file creation to prevent Jekyll processing (05e9fc6)

Changes in v0.99.11

Bug Fixes

  • use JamesIves/github-pages-deploy-action instead (65dc2bd)

Changes in v0.99.10

Bug Fixes

  • add github-pages environment to pkgdown workflow (f2c20ef)

Changes in v0.99.9

Bug Fixes

  • configure BiocParallel for serial processing in tests (e8b3979)
  • correct example code and cross-references (bd86c11)

Changes in v0.99.8

Bug Fixes

  • doc: also used filtering for original function (a43eaa5)
  • polygon type now matches original XCMS behavior exactly (418668e)
  • update tests to handle chromatograms without peaks correctly (670a477)

Changes in v0.99.7

Bug Fixes

  • use GitHub Pages artifact deployment for pkgdown (1ce3fc8)

Changes in v0.99.6

Bug Fixes

  • add complete example for ghighlightChromPeaks (0a27bf1)

Changes in v0.99.5

Bug Fixes

  • ensure .nojekyll file is created for pkgdown site (29eb82c)
  • resolve R CMD check warnings in gplot (86345f2)
  • update prepare-news.sh path in release workflow (f04ed39)

Changes in v0.99.4

Bug Fixes

  • highlightChromPeaks only works for XCMSnExp (ebb1851)
  • refactor gplot and ghighlightChromPeaks per code review (14fb0de)
  • remove library(xcmsVis) from vignettes for R CMD check (0d1aad6)
  • restore library(xcmsVis) in vignette (070bae0)
  • reverse viridis scale in gplotChromPeakImage to match XCMS (049d978)

Features

  • add gplot() method for XChromatogram objects (9dbbc33)

Changes in v0.99.3

Bug Fixes

  • constrain version to 0.99.x for Bioconductor development (5de5bfd)
  • correct NEWS.md to use 0.99.x versioning (f0978fd)

Changes in v0.99.2

Features

  • add gplotChromPeaks, gplotChromPeakImage, and ghighlightChromPeaks (0893bfa)
  • add SystemRequirements for Quarto vignettes (498afc6)
  • add comprehensive vignette for peak visualization functions

Bug Fixes

  • constrain version to 0.99.x for Bioconductor development
    1. convert from MsExperiment to XcmsExperiment to skip the peak picking (707aadb)
  • account for OnDiskMSnExp and get filenames if not in pData. (b1af112)
  • add BiocParallel to Suggests and fix fileNames import (69fb33e)
  • add missing dplyr::n import to utils.R (dd8b918)
  • add Quarto setup to GitHub Actions workflows
  • address BiocCheck requirements (b1c4d5f)
  • coerce instead of new peakpicking (159c06a)
  • consistency of objects (5e52665)
  • correct version ordering in NEWS.md (026dbcf)
  • corrected tests. (3b61b79)
  • properly import is() from methods package (4086c92)
  • remove BPPARAM from groupChromPeaks calls (26eec03)
  • remove links from NEWS.md headings for pkgdown compatibility (8262eec)
  • remove unused methods from Imports (358535b)
  • resolve R CMD check warnings (d892e19)
  • use SerialParam in tests to avoid parallel processing warnings (abbfb4f)

Performance Improvements

  • use SerialParam in vignette for faster processing (382f301)

Changes in v0.99.0

Bug Fixes

    1. provide spectraOrigin_base for matching column names and omit files filtered away after alignment. (8aceeae)
  • actually working version of gplotAdjustedRtime that for now works on XcmsExperiment objects. some imports missing. will fix later (5f9898c)
  • add groupChromPeaks after filterFile in tests (73b30f4)
  • add MSnbase to Imports and fix missing global variables (772346e)
  • correct test fixtures and helper functions for dual-class support (cf9b1bd)
  • exclude quarto cache from R package builds (764d68f)
  • fixed .get_spectra_data to ahve the same columns (75b2b2b)
  • fixed imports in gplotAdjustedRtime (39aa2b3)
  • re-add groupChromPeaks after filterFile in vignette (fe46d99)
  • replace Quarto columns with HTML flexbox for pkgdown compatibility (646b3ef)

Features

  • add comprehensive alt-text to all vignette figures (89a33aa)
  • add comprehensive testing and documentation for gplotAdjustedRtime (552315e)
  • add helper function to get spectra data from both object types (47038d7)

Changes in v0.2.0

Bug Fixes

  • correct GitHub Actions workflow and vignette workflow (6dd52fd)

Features

  • add semantic versioning and improve package infrastructure (86a0704)

Changes in v0.1.0

Features

  • Support for both XCMSnExp and XcmsExperiment objects
  • Add utility functions for object type handling (.get_sample_data, .validate_xcms_object)
  • Comprehensive test suite with faahKO example data
  • Working vignette with executable code examples using faahKO data
  • pkgdown documentation site

Bug Fixes

  • Fix vignette to use real data instead of eval=FALSE examples
  • Update sample metadata extraction to handle both object types correctly

Changes in v0.0.1

Features

  • Initial release
  • Implement gplotAdjustedRtime() function
  • ggplot2 visualization of retention time adjustment
  • Interactive tooltip support for plotly
  • Complete package infrastructure (CI/CD, documentation, tests)
  • Comparison vignette showing XCMS vs xcmsVis approaches