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obs. vs. obs for all grouped plots using BasePlot#2769

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yugeji wants to merge 28 commits into
scverse:mainfrom
yugeji:master
Open

obs. vs. obs for all grouped plots using BasePlot#2769
yugeji wants to merge 28 commits into
scverse:mainfrom
yugeji:master

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@yugeji

@yugeji yugeji commented Nov 28, 2023

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  • Closes #1876 and reimplements stale PR #2055 zhangguy:dotplot2d
  • Empty group currently breaks
  • dendrogram doesn't work with all plots
  • I don't think anything would break if you just removed var_name reordering from the dendrogram entirely
  • add tests using groupby_cols params
  • Docs!

@codecov

codecov Bot commented Nov 28, 2023

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Codecov Report

Attention: Patch coverage is 54.23729% with 27 lines in your changes are missing coverage. Please review.

Project coverage is 75.12%. Comparing base (6542113) to head (1c4740e).

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2769      +/-   ##
==========================================
- Coverage   75.24%   75.12%   -0.13%     
==========================================
  Files         116      116              
  Lines       12802    12847      +45     
==========================================
+ Hits         9633     9651      +18     
- Misses       3169     3196      +27     
Files Coverage Δ
scanpy/plotting/_anndata.py 84.98% <100.00%> (ø)
scanpy/plotting/_docs.py 100.00% <ø> (ø)
scanpy/plotting/_tools/__init__.py 77.28% <ø> (ø)
scanpy/testing/_helpers/__init__.py 100.00% <100.00%> (ø)
scanpy/plotting/_matrixplot.py 95.69% <66.66%> (-1.01%) ⬇️
scanpy/plotting/_dotplot.py 91.28% <71.42%> (-0.61%) ⬇️
scanpy/plotting/_stacked_violin.py 81.48% <62.50%> (-3.02%) ⬇️
scanpy/plotting/_baseplot_class.py 86.47% <34.78%> (-3.42%) ⬇️

@ivirshup
ivirshup self-requested a review January 11, 2024 15:35
@flying-sheep
flying-sheep requested review from flying-sheep and removed request for ivirshup February 22, 2024 15:37
@flying-sheep flying-sheep added this to the 1.11.0 milestone Mar 18, 2024
Comment on lines +478 to +483
# _matrix.columns = [f"{x}_{idx}" for idx, x in enumerate(_matrix.columns)] # added warning as this row was commented out
if _matrix.columns.value_counts().max() > 1:
warn(
"Duplicate gene or condition labels present."
"Results might be unexpected."
)

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@yugeji commenting this out doesn’t work with newer pandas versions anymore. Does your branch handle duplicated columns? Then we can just move this into the if len(self.groupby_cols) < 1: branch

@flying-sheep flying-sheep modified the milestones: 1.11.0, 1.12.0 Dec 20, 2024
@flying-sheep flying-sheep modified the milestones: 1.12.0, 1.13.0 Jan 23, 2026
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4 participants