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Fix rank_genes_groups_violin’s gene_symbols #2554

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Fix rank_genes_groups_violin’s gene_symbols #2554

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83ff832
Add failing test
flying-sheep Jul 11, 2023
29c6a08
Merge branch 'master' into fix-rank-gene-groups-violin-gene-symbols
flying-sheep Jul 27, 2023
a4341a0
smaller test data
flying-sheep Jul 31, 2023
0dda284
Merge branch 'main' into fix-rank-gene-groups-violin-gene-symbols
flying-sheep Jan 13, 2025
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Binary file added tests/_data/t-cells.h5ad
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19 changes: 19 additions & 0 deletions tests/test_rank_genes_groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -307,6 +307,25 @@ def test_wilcoxon_tie_correction(reference):
np.testing.assert_allclose(test_obj.stats[groups[0]]["pvals"], pvals)


def test_rank_gene_groups_violin_gene_symbols():
adata = sc.read_h5ad(DATA_PATH / "t-cells.h5ad")

t_celltypes = ["Naive CD4+ T cells", "Naive CD8+ T cells"]
sc.tl.rank_genes_groups(
adata,
groupby="cell_type",
groups=t_celltypes,
reference="rest",
method="wilcoxon",
use_raw=False,
)

# We get the KeyError here
sc.pl.rank_genes_groups_violin(
adata, groups=t_celltypes, n_genes=15, strip=False, gene_symbols="gene_symbols"
)


def test_wilcoxon_huge_data(monkeypatch):
max_size = 300
adata = pbmc68k_reduced()
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