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Fix augur low frequency cell type behavior #938

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Merged
Zethson merged 2 commits into from
Mar 19, 2026
Merged

Fix augur low frequency cell type behavior #938

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f3bd9fd
Fix augur low frequency cell type behavior
Zethson Mar 19, 2026
826cc63
Fix augur low frequency cell type behavior
Zethson Mar 19, 2026
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2 changes: 1 addition & 1 deletion docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@
"mudata": ("https://mudata.readthedocs.io/stable/", None),
"matplotlib": ("https://matplotlib.org/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
"pandas": ("https://pandas.pydata.org/docs/", None),
"python": ("https://docs.python.org/3", None),
"scipy": ("https://docs.scipy.org/doc/scipy/", None),
"scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
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3 changes: 2 additions & 1 deletion pertpy/tools/_augur.py
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Expand Up @@ -792,7 +792,8 @@ def predict(
adata.obs["augur_score"] = nan
for cell_type in track(adata.obs["cell_type"].unique(), description="Processing data..."):
cell_type_subsample = adata[adata.obs["cell_type"] == cell_type].copy()
if augur_mode in ("default", "permute"):

if augur_mode in ("default", "permute") and len(cell_type_subsample) >= min_cells:
cell_type_subsample = (
self.select_highly_variable(cell_type_subsample)
if not select_variance_features
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