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docs: add inline example plot to sc.pl.highly_variable_genes#4032

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flying-sheep merged 3 commits intoscverse:mainfrom
Ekin-Kahraman:docs/inline-example-highly-variable-genes
Apr 7, 2026
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docs: add inline example plot to sc.pl.highly_variable_genes#4032
flying-sheep merged 3 commits intoscverse:mainfrom
Ekin-Kahraman:docs/inline-example-highly-variable-genes

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@Ekin-Kahraman
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Adds an Examples section to the sc.pl.highly_variable_genes docstring with two inline plot blocks:

  1. Minimal pipeline: load PBMC 3k, normalise, log-transform, compute HVGs, plot
  2. Same data with log=True to demonstrate the parameter

Uses sc.datasets.pbmc3k() and :context: close-figs following the pattern from merged contributions to the #1664 checklist.

Checklist item from #1664.

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codecov bot commented Apr 5, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.51%. Comparing base (dbb5c58) to head (2aad5b8).
⚠️ Report is 1 commits behind head on main.
✅ All tests successful. No failed tests found.

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##             main    #4032   +/-   ##
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  Coverage   78.51%   78.51%           
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  Files         117      117           
  Lines       12753    12753           
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  Hits        10013    10013           
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Flag Coverage Δ
hatch-test.low-vers 77.80% <ø> (ø)
hatch-test.pre 77.47% <ø> (ø)

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Files with missing lines Coverage Δ
src/scanpy/plotting/_preprocessing.py 86.27% <ø> (ø)

@flying-sheep flying-sheep added this to the 1.12.1 milestone Apr 7, 2026
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flying-sheep commented Apr 7, 2026

Hi thank you for your contribution!

Please next time don’t delete the PR template, but fill it out instead.

also looks like @haoyu-haoyu had the same idea a bit earlier in #4025, but you use the right preprocessing. https://icb-scanpy--4032.com.readthedocs.build/en/4032/api/generated/scanpy.pl.highly_variable_genes.html

@flying-sheep flying-sheep merged commit c7c1f4e into scverse:main Apr 7, 2026
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meeseeksmachine pushed a commit to meeseeksmachine/scanpy that referenced this pull request Apr 7, 2026
flying-sheep pushed a commit that referenced this pull request Apr 7, 2026
…sc.pl.highly_variable_genes) (#4034)

Co-authored-by: Ekin Kahraman <wf9xpgccxy@privaterelay.appleid.com>
@flying-sheep flying-sheep mentioned this pull request Apr 7, 2026
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2 participants