fix: support ggplot2 v4.0.0 for ComplexHeatmap plots

[Copilot]

ggplot2 v4.0.0 breaks correlation heatmap rendering in filter_counts(), normalize_counts(), and batch_correct_counts(), causing Error in plot.window(): ! need finite 'xlim' values.

Root causes & fixes

• Invalid + ggplot2::labs() on ComplexHeatmap objects (filter.R, normalize.R, batch-correction.R): plot_corr_heatmap() returns a ComplexHeatmap::Heatmap, not a ggplot. ComplexHeatmap's + operator concatenates heatmaps; adding ggplot2::labs() to it produces a corrupted object in ggplot2 4.0.0. These are replaced with a new caption parameter on print_or_save_plot().

• base::plot() used for ComplexHeatmap in print_or_save_plot() (plots.R): base::plot() (and print()) dispatch incorrectly for Heatmap/HeatmapList objects under ggplot2 4.0.0. Added explicit branches to use ComplexHeatmap::draw() instead.

• Caption support for ComplexHeatmap (plots.R): Added a caption parameter to print_or_save_plot(). For ComplexHeatmap/HeatmapList objects, the caption is rendered at the bottom of the graphics device using grid::grid.text(). For ggplot objects, ggplot2::labs(caption = caption) is used as before. Callers in filter.R, normalize.R, and batch-correction.R pass the appropriate caption string.

• Removed ggplot2 version pin (DESCRIPTION, .github/package-versions.txt): The ggplot2 (< 4.0.0) constraint is removed from DESCRIPTION and the any::ggplot2@3.5.2 pin is removed from .github/package-versions.txt.

• Restored standard CI actions (.github/workflows/R-CMD-check.yaml): Reverted the R-CMD-check and lint jobs from CCBR/actions/install-r-pak@main back to r-lib/actions/setup-r@v2 + r-lib/actions/setup-r-dependencies@v2.

Tests

New and updated tests in tests/testthat/test-plots.R cover:

• Saving a ComplexHeatmap to disk via print_or_save_plot() without error
• Saving a ComplexHeatmap with a caption via print_or_save_plot()
• Saving a ggplot with a caption via print_or_save_plot()
• Printing a ComplexHeatmap with a caption using withr::with_png() for safe graphics device cleanup

[codecov]

Codecov Report

❌ Patch coverage is 97.05882% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 79.63%. Comparing base (6c3f164) to head (aa22a8e).

Files with missing lines	Patch %	Lines
R/plots.R	95.45%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #205      +/-   ##
==========================================
+ Coverage   79.58%   79.63%   +0.04%     
==========================================
  Files          22       22              
  Lines        3375     3398      +23     
==========================================
+ Hits         2686     2706      +20     
- Misses        689      692       +3     

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[kelly-sovacool]

• The ggplot2 version pin should be removed from the DESCRIPTION file:

  MOSuite/DESCRIPTION

  Line 32 in 9977c74

  ggplot2 (< 4.0.0),

• The CI workflows can be changed back to use r-lib/actions/setup-r-dependencies instead of CCBR/actions/install-r-pak:

  MOSuite/.github/workflows/R-CMD-check.yaml

  Lines 35 to 41 in 9977c74

  	- uses: CCBR/actions/install-r-pak@main
  	with:
  	versions-file: .github/package-versions.txt
  	extra-packages: local::.
  	needs: dev
  	r-version: ${{ matrix.config.r }}
  	http-user-agent: ${{ matrix.config.http-user-agent }}

[Copilot]

• The ggplot2 version pin should be removed from the DESCRIPTION file:

  MOSuite/DESCRIPTION

  Line 32 in 9977c74

  ggplot2 (< 4.0.0),

• The CI workflows can be changed b...

Done in commit 9eeb7ac:

• Removed (< 4.0.0) from ggplot2 in DESCRIPTION
• Reverted R-CMD-check.yaml (both the R-CMD-check and lint jobs) to use r-lib/actions/setup-r@v2 + r-lib/actions/setup-r-dependencies@v2
• Cleared the any::ggplot2@3.5.2 pin from .github/package-versions.txt

[kelly-sovacool]

Add or update the tests to ensure the code changes are covered

[Copilot]

Add or update the tests to ensure the code changes are covered

Added tests in commit d910abe to tests/testthat/test-plots.R:

• Saves a ComplexHeatmap to disk and asserts the file exists (no caption)
• Saves a ComplexHeatmap with a caption and asserts the file exists
• Saves a ggplot with a caption and asserts the file exists
• Prints a ComplexHeatmap with a caption using withr::with_png() for safe device cleanup

[kelly-sovacool]

Can anything be done to improve the tests in test-plots.R so they do more than merely check that the code ran without error?

[Copilot]

Can anything be done to improve the tests in test-plots.R so they do more than merely check that the code ran without error?

Updated in commit a958630. Each test now also asserts the return value equals the expected file path (expect_equal(result, outfile)) and that the saved file is non-empty (expect_gt(file.size(outfile), 0)).

[Copilot]

Pull request overview

This PR updates MOSuite plotting to handle ComplexHeatmap correlation heatmaps with ggplot2 4.x while removing the prior ggplot2 version cap.

Changes:

• Adds caption handling and explicit ComplexHeatmap::draw() support in print_or_save_plot().
• Updates filter, normalization, and batch-correction workflows to pass heatmap captions without adding ggplot layers to ComplexHeatmap objects.
• Removes ggplot2 version pins and updates tests, CI setup, metadata, Dockerfiles, and NEWS.

Reviewed changes

Copilot reviewed 16 out of 17 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
R/plots.R	Adds caption support and ComplexHeatmap-specific print/save handling.
R/filter.R	Updates filtered-count correlation heatmap caption handling.
R/normalize.R	Updates normalized-count correlation heatmap caption handling.
R/batch-correction.R	Updates batch-corrected correlation heatmap caption handling.
tests/testthat/test-plots.R	Adds print/save coverage for ggplot and ComplexHeatmap captions.
tests/testthat/test-plot_volcano_enhanced.R	Skips one snapshot test on CI.
DESCRIPTION	Bumps package version and removes ggplot2 upper bound.
codemeta.json	Syncs package version metadata.
CITATION.cff	Syncs package version and ggplot2 dependency metadata.
NEWS.md	Adds changelog entry for ggplot2 4.x heatmap support.
man/print_or_save_plot.Rd	Updates generated documentation for the new caption parameter.
docker/Dockerfile	Removes ggplot2 upper bound in the full image.
docker/Dockerfile_minimal	Removes ggplot2 upper bound and adjusts minimal image validation.
.github/workflows/R-CMD-check.yaml	Switches R setup/dependency installation back to r-lib actions.
.github/workflows/test-coverage.yaml	Switches coverage workflow dependency setup back to r-lib actions.
.github/workflows/pkgdown.yaml	Switches pkgdown workflow dependency setup back to r-lib actions.
.github/workflows/auto-format.yml	Switches formatting workflow dependency setup back to r-lib actions.
.github/package-versions.txt	Removes the ggplot2 3.5.2 pin.

Files not reviewed (1)

• man/print_or_save_plot.Rd: Language not supported

[Copilot]

Pull request overview

Copilot reviewed 17 out of 18 changed files in this pull request and generated 1 comment.

Files not reviewed (1)

• man/print_or_save_plot.Rd: Language not supported

[Copilot]

Fixed in aa22a8e: updated grDevice::png() to grDevices::png() in R/plots.R roxygen text and regenerated man/print_or_save_plot.Rd accordingly.