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missing var_names in BasePlot #3460

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FrancescaDr
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  • Release notes not necessary because:

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codecov bot commented Feb 10, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.45%. Comparing base (cce4bd6) to head (73f6c0b).

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #3460   +/-   ##
=======================================
  Coverage   75.44%   75.45%           
=======================================
  Files         113      113           
  Lines       13250    13254    +4     
=======================================
+ Hits         9997    10001    +4     
  Misses       3253     3253           
Files with missing lines Coverage Δ
src/scanpy/plotting/_baseplot_class.py 91.64% <100.00%> (+0.09%) ⬆️

@flying-sheep
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Hi! var_names can’t just contain values from .var.index, but also other sources, handled by

sc.get.obs_df(adata, keys=keys, layer=layer, use_raw=use_raw, gene_symbols=gene_symbols)

One approach could be to add a warn_only: bool = False parameter to .sc.get.obs_df which could then be specified in the plotting function.

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"Interactive" Dotplot version: check for available var_names
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