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Add **kwargs in umap to allow other parameters in UMAP. #222

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merged 2 commits into from
Feb 4, 2024
Merged

Add **kwargs in umap to allow other parameters in UMAP. #222

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f8e9be1
Add **kwargs in umap to allow other parameters in UMAP.
beyondpie Jan 24, 2024
8b52bfc
minor
beyondpie Jan 24, 2024
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11 changes: 8 additions & 3 deletions snapatac2-python/snapatac2/tools/_embedding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def umap2(
Random seed.
inplace
Whether to store the result in the anndata object.

Returns
-------
np.ndarray | None
Expand Down Expand Up @@ -68,6 +68,7 @@ def umap(
key_added: str = 'umap',
random_state: int = 0,
inplace: bool = True,
**kwargs
) -> np.ndarray | None:
"""
Parameters
Expand All @@ -86,6 +87,8 @@ def umap(
Random seed.
inplace
Whether to store the result in the anndata object.
**kwargs
Other parameters defined in umap.UMAP

Returns
-------
Expand All @@ -101,7 +104,9 @@ def umap(
if use_dims is not None:
data = data[:, :use_dims] if isinstance(use_dims, int) else data[:, use_dims]

umap = UMAP(random_state=random_state, n_components=n_comps).fit_transform(data)
umap = UMAP(random_state=random_state,
n_components=n_comps,
**kwargs).fit_transform(data)
if inplace:
adata.obsm["X_" + key_added] = umap
else:
Expand Down Expand Up @@ -518,4 +523,4 @@ def multi_spectral(
evals = evals[idx]
evecs = evecs[:, idx] * np.sqrt(evals)

return (evals, evecs)
return (evals, evecs)
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