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Can now specify which 'layer' of the AnnData table to use #402

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merged 11 commits into from
Jan 20, 2025

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Sonja-Stockhaus
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Should solve #326

Plus: 2 bugfixes when coloring points by values in a table:
a) coloring by values in table.X didn't work before
b) Error when using the groups argument while the values to color by are stored in a table

@Sonja-Stockhaus Sonja-Stockhaus linked an issue Jan 7, 2025 that may be closed by this pull request
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This PR depends on scverse/spatialdata#818

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Sonja-Stockhaus commented Jan 7, 2025

Todo:

  • Delete utils.get_values_point_table()? Fully use spatialdata's get_values()
  • Tests

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codecov-commenter commented Jan 13, 2025

Codecov Report

Attention: Patch coverage is 85.48387% with 9 lines in your changes missing coverage. Please review.

Project coverage is 83.83%. Comparing base (12f490d) to head (c5d0c42).
Report is 4 commits behind head on main.

Files with missing lines Patch % Lines
src/spatialdata_plot/pl/utils.py 77.50% 9 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #402      +/-   ##
==========================================
+ Coverage   83.76%   83.83%   +0.06%     
==========================================
  Files           8        8              
  Lines        1694     1732      +38     
==========================================
+ Hits         1419     1452      +33     
- Misses        275      280       +5     
Files with missing lines Coverage Δ
src/spatialdata_plot/pl/basic.py 89.26% <ø> (ø)
src/spatialdata_plot/pl/render.py 91.16% <100.00%> (+0.38%) ⬆️
src/spatialdata_plot/pl/render_params.py 100.00% <100.00%> (ø)
src/spatialdata_plot/pl/utils.py 78.00% <77.50%> (-0.09%) ⬇️

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Sonja-Stockhaus commented Jan 14, 2025

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@LucaMarconato this PR is waiting for the next SpatialData release - do you have an ETA for that?

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@LucaMarconato this PR is waiting for the next SpatialData release - do you have an ETA for that?

Yes, today 😁

@timtreis timtreis changed the title layer selection when coloring by values in a table Can now specify which 'layer' of the AnnData table to use Jan 20, 2025
@timtreis timtreis marked this pull request as ready for review January 20, 2025 16:39
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Added validation function, otherwise lgtm

@timtreis timtreis merged commit 16aa9e9 into main Jan 20, 2025
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@LucaMarconato LucaMarconato deleted the feature/issue326-layer-selection-of-anndata branch January 20, 2025 17:08
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Cannot pass layer selection of anndata
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