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Fix getting log1p base #2546

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merged 2 commits into from
Jul 7, 2023
Merged

Fix getting log1p base #2546

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2337f56
safe get log1p base
sshen8 Jul 6, 2023
8d278bd
add test
flying-sheep Jul 7, 2023
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2 changes: 1 addition & 1 deletion scanpy/preprocessing/_highly_variable_genes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,7 @@ def _highly_variable_genes_single_batch(
"""
X = adata.layers[layer] if layer is not None else adata.X
if flavor == 'seurat':
if 'log1p' in adata.uns_keys() and adata.uns['log1p']['base'] is not None:
if 'log1p' in adata.uns_keys() and adata.uns['log1p'].get('base') is not None:
X *= np.log(adata.uns['log1p']['base'])
X = np.expm1(X)

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15 changes: 15 additions & 0 deletions scanpy/tests/test_rank_genes_groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -248,6 +248,21 @@ def test_emptycat():
rank_genes_groups(pbmc, groupby='louvain')


def test_log1p_save_restore(tmp_path):
"""tests the sequence log1p→save→load→rank_genes_groups"""
from anndata import read

pbmc = pbmc68k_reduced()
sc.pp.log1p(pbmc)

path = tmp_path / 'test.h5ad'
pbmc.write(path)

pbmc = read(path)

sc.tl.rank_genes_groups(pbmc, groupby='bulk_labels', use_raw=True)


def test_wilcoxon_symmetry():
pbmc = pbmc68k_reduced()

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4 changes: 2 additions & 2 deletions scanpy/tools/_rank_genes_groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ def __init__(
layer=None,
comp_pts=False,
):
if 'log1p' in adata.uns_keys() and adata.uns['log1p']['base'] is not None:
if 'log1p' in adata.uns_keys() and adata.uns['log1p'].get('base') is not None:
self.expm1_func = lambda x: np.expm1(x * np.log(adata.uns['log1p']['base']))
else:
self.expm1_func = np.expm1
Expand Down Expand Up @@ -751,7 +751,7 @@ def filter_rank_genes_groups(
index=gene_names.index,
)

if 'log1p' in adata.uns_keys() and adata.uns['log1p']['base'] is not None:
if 'log1p' in adata.uns_keys() and adata.uns['log1p'].get('base') is not None:
expm1_func = lambda x: np.expm1(x * np.log(adata.uns['log1p']['base']))
else:
expm1_func = np.expm1
Expand Down