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Updated Harmony Integrate Docs to better match interface to Harmonypy package #3362

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merged 8 commits into from
Nov 19, 2024
Merged

Updated Harmony Integrate Docs to better match interface to Harmonypy package #3362

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f7e0ec4
Update _harmony_integrate.py
DaminK Nov 12, 2024
109b68e
Include Sequence type
DaminK Nov 12, 2024
53c19d8
Small typo
DaminK Nov 12, 2024
a9ccc04
Removed trailing whitespace
DaminK Nov 12, 2024
80ff229
type cheking block
DaminK Nov 12, 2024
4bab766
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 19, 2024
6034b37
change log
flying-sheep Nov 19, 2024
99aa9da
Merge branch 'main' into harmony_doc_fix
flying-sheep Nov 19, 2024
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1 change: 1 addition & 0 deletions docs/release-notes/3362.doc.md
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@@ -0,0 +1 @@
Improve {func}`~scanpy.external.pp.harmony_integrate` docs {smaller}`D Kühl`
7 changes: 5 additions & 2 deletions src/scanpy/external/pp/_harmony_integrate.py
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Expand Up @@ -4,6 +4,7 @@

from __future__ import annotations

from collections.abc import Sequence # noqa: TCH003
from typing import TYPE_CHECKING

import numpy as np
Expand All @@ -19,7 +20,7 @@
@doctest_needs("harmonypy")
def harmony_integrate(
adata: AnnData,
key: str,
key: str | Sequence[str],
*,
basis: str = "X_pca",
adjusted_basis: str = "X_pca_harmony",
Expand All @@ -42,7 +43,9 @@ def harmony_integrate(
The annotated data matrix.
key
The name of the column in ``adata.obs`` that differentiates
among experiments/batches.
among experiments/batches. To integrate over two or more covariates,
you can pass multiple column names as a list. See ``vars_use``
parameter of the ``harmonypy`` package for more details.
basis
The name of the field in ``adata.obsm`` where the PCA table is
stored. Defaults to ``'X_pca'``, which is the default for
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