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Add gene filtering functionality and enhance label handling#36

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alsmith151 merged 3 commits into
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feat/add-filter-by-gene-name
May 27, 2026
Merged

Add gene filtering functionality and enhance label handling#36
alsmith151 merged 3 commits into
mainfrom
feat/add-filter-by-gene-name

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This pull request introduces several documentation enhancements and API improvements, primarily focused on gene annotation handling, new visualization options, and usability tweaks for the plotnado package. The changes make it easier to use gene annotations from multiple sources, add new plotting features, and adjust default visual behaviors for improved clarity.

Documentation improvements:

  • Added detailed instructions for using gene annotations from bundled, registered, or direct file sources, including how to download from UCSC GoldenPath and filter to specific genes with gene_filter.
  • Expanded documentation with new sections on signal smoothing, threshold/coordinate markers, BigWig difference options, BigWig collection styles, gene label strategies, and human-readable axis labels, each with usage examples and option tables.

API and usability enhancements:

  • Added gene_filter as a supported keyword argument for gene tracks, allowing users to restrict displayed genes by name. This is reflected in both the GenesKwargs type and the GenomicFigure interface. [1] [2]
  • Changed default values for several visual options in GenomicFigure (as seen in the .pyi interface): labels are now shown on tracks by default (label_on_track=True), label box alpha is slightly reduced for less obtrusive backgrounds (label_box_alpha=0.85), and label offsets are adjusted for improved spacing. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14]

Codebase and minor documentation tweaks:

  • Improved separator rendering logic in figure.py to skip drawing between adjacent Genes and ScaleBar tracks, simplifying the code and preventing unnecessary separators.
  • Ensured code examples in the option lookup documentation are not echoed in output, making the docs cleaner. [1] [2]

@alsmith151

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Fixes #20

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codecov-commenter commented May 27, 2026

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⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 98.18182% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 79.36%. Comparing base (5f934ad) to head (eb49bee).

Files with missing lines Patch % Lines
plotnado/tracks/scaling.py 93.33% 1 Missing ⚠️
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Additional details and impacted files
@@            Coverage Diff             @@
##             main      #36      +/-   ##
==========================================
+ Coverage   79.09%   79.36%   +0.27%     
==========================================
  Files          42       42              
  Lines        5554     5588      +34     
==========================================
+ Hits         4393     4435      +42     
+ Misses       1161     1153       -8     

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@alsmith151 alsmith151 merged commit 800e26e into main May 27, 2026
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@alsmith151 alsmith151 deleted the feat/add-filter-by-gene-name branch May 27, 2026 15:26
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2 participants