Updated MoleculeRankPlot

[ludvigla]

Description

This PR updates MoleculeRankPlot to enable:

• highlight min/max size filter (horizontal dashed lines)
• highlight numbers of cells per size category: Low, Normal, High
• add "rug" density distribution
• split plots by group_by column

Fixes: PNA-2283

Type of change

• Bug fix (non-breaking change which fixes an issue).
• New feature (non-breaking change which adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

How Has This Been Tested?

Updated tests in tests/testthat/test-MoleculeRankPlot.R

PR checklist:

• My changes generate no new warnings.
• I have added tests that prove my fix is effective or that my feature works.
• I have documented any significant changes to the code in CHANGELOG.md

[codecov-commenter]

Codecov Report

❌ Patch coverage is 95.23810% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.37%. Comparing base (9be38ba) to head (4c990aa).

Files with missing lines	Patch %	Lines
R/molecule_rank_plot.R	95.14%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #144      +/-   ##
==========================================
+ Coverage   80.20%   80.37%   +0.16%     
==========================================
  Files          56       56              
  Lines        8296     8392      +96     
==========================================
+ Hits         6654     6745      +91     
- Misses       1642     1647       +5     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR enhances MoleculeRankPlot to support additional QC annotations (min/max threshold lines, category cell counts, rug distribution) and optional faceting by a group_by column, with corresponding documentation and tests.

Changes:

• Added new MoleculeRankPlot parameters: n_umi_min_threshold, n_umi_max_threshold, highlight_cell_counts, rug, and split (faceting).
• Extended type-check utilities to allow assert_within_limits(..., allow_null = TRUE) for optional numeric inputs.
• Updated docs, NAMESPACE imports (ggplot2 geom_rug), tests, and CHANGELOG entry.

Reviewed changes

Copilot reviewed 8 out of 10 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
R/molecule_rank_plot.R	Implements new plot features, input validation, faceting, rug, and cell-count annotations.
R/types_check.R	Adds allow_null support to assert_within_limits() to validate optional numeric thresholds.
R/generics.R	Updates MoleculeRankPlot roxygen docs for new parameters/behavior.
R/pixelatorR-package.R	Adds roxygen import for ggplot2::geom_rug.
NAMESPACE	Imports geom_rug from ggplot2.
man/type_check_helpers.Rd	Regenerates docs reflecting the updated assert_within_limits() signature.
man/MoleculeRankPlot.Rd	Regenerates docs reflecting new MoleculeRankPlot arguments and updated examples.
tests/testthat/test-MoleculeRankPlot.R	Adds tests covering new arguments and split/facet behavior.
CHANGELOG.md	Notes the new MoleculeRankPlot capabilities.

Files not reviewed (2)

• man/MoleculeRankPlot.Rd: Generated file
• man/type_check_helpers.Rd: Generated file

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[maxkarlsson]

Looks good! Found 1 potential bug and had two comments.

[maxkarlsson]

We could make it simpler and just set this to n_umi_min_threshold and use vjust to control positioning (?)

[ludvigla]

Yeah that works too, but I felt it was more boiler plate code because I had to add multiple geom_text layer. I made some AI-powered improvements which should be more robust.