Add gene_symbols parameter to render_shapes, render_points, render_labels#578
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Add gene_symbols parameter to render_shapes, render_points, render_labels#578
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…bels (#247) Allow coloring by gene symbols when var_names are ENSEMBL IDs, mirroring scanpy's gene_symbols parameter. When provided, the code looks up the color key in the specified adata.var column and maps it back to the actual var_name before proceeding with the normal rendering pipeline. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Avoid mutating col_for_color inside the auto-detect loop — resolve gene symbol to var_name only once after the table is selected. Add non-visual tests for the auto-detect path, missing symbol, and missing column error cases. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…t loop Avoid calling _resolve_gene_symbols twice for the winning table by caching the result during the filtering loop. Add a warning when a gene symbol maps to multiple var_names. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Generated from CI runner (py3.11-stable). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #578 +/- ##
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+ Coverage 75.36% 75.51% +0.15%
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Files 10 10
Lines 2935 2986 +51
Branches 684 699 +15
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+ Hits 2212 2255 +43
- Misses 441 445 +4
- Partials 282 286 +4
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Summary
gene_symbolsparameter torender_shapes(),render_points(), andrender_labels(), mirroring scanpy's established patternvar_namesare ENSEMBL IDs, users can now color by gene symbols stored in avarcolumn (e.g.,color="TP53", gene_symbols="gene_symbol")gene_symbols=None(default) preserves all existing behaviorCloses #247
How it works
When
color="TP53"isn't found inobs.columnsorvar_names, andgene_symbols="gene_symbol"is provided, the code looks up"TP53"inadata.var["gene_symbol"], maps it to the corresponding var_name (index), and proceeds with normal rendering. This happens in_validate_col_for_column_table()via a new_resolve_gene_symbols()helper.