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Drop unused categories in ExperimentAxisQuery.to_anndata #204

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merged 5 commits into from
Jul 24, 2024
Merged

Drop unused categories in ExperimentAxisQuery.to_anndata #204

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b1ac482
Drop unused categories in `ExperimentAxisQuery.to_anndata`
nguyenv Jul 24, 2024
c6e5db1
format
nguyenv Jul 24, 2024
24a0275
opt-in for dropping categories
nguyenv Jul 24, 2024
121c642
Add desc
nguyenv Jul 24, 2024
b98915e
Update python-spec/src/somacore/query/query.py with desc change
nguyenv Jul 24, 2024
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12 changes: 11 additions & 1 deletion python-spec/src/somacore/query/query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -298,7 +298,7 @@ def to_anndata(

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Let's add a description of what drop_levels does ...

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@pablo-gar @eddelbuettel @mojaveazure are you okay with drop_levels?

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(Presuming we'll want a same-ish name in Python & R both ...)

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Seurat uses drop to match R, but I'm fine with drop_levels in SOMA

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Sounds good to me!

Lifecycle: maturing
"""
return self._read(
ad = self._read(
X_name,
column_names=column_names or AxisColumnNames(obs=None, var=None),
X_layers=X_layers,
Expand All @@ -308,6 +308,16 @@ def to_anndata(
varp_layers=varp_layers,
).to_anndata()

# Drop unused categories on axis dataframes
for name in ad.obs:
if pd.api.types.is_categorical_dtype(ad.obs[name]):
ad.obs[name] = ad.obs[name].cat.remove_unused_categories()
for name in ad.var:
if pd.api.types.is_categorical_dtype(ad.var[name]):
ad.var[name] = ad.var[name].cat.remove_unused_categories()

return ad

# Context management

def close(self) -> None:
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