Integration

mina.integration.patpy.PrecomputedSampleRepresentation

Bases: SampleRepresentationMethod

Wrap a precomputed sample-by-feature matrix for patpy tools.

This is useful when sample-level representations were computed outside patpy, for example using MINA, MOFA, PCA, or another latent-variable model.

Parameters:

Name	Type	Description	Default
representation	DataFrame	DataFrame with samples in rows and latent variables/features in columns.	required
metadata	DataFrame or None	Optional sample-level metadata. Its index must contain the same sample IDs as representation.index.	None
metric	str	Distance metric passed to scipy.spatial.distance.pdist.	'euclidean'
seed	int	Random seed used by patpy embedding methods.	67

prepare_anndata(adata=None)

Skip AnnData preparation.

Parameters:

Name	Type	Description	Default
adata	AnnData or None	Ignored placeholder for compatibility with the patpy interface.	None

Returns:

Type	Description
None	The representation is already sample-level and no preparation is needed.

calculate_distance_matrix(force: bool = False, dist: str | None = None) -> np.ndarray

Calculate a sample-by-sample distance matrix.

Parameters:

Name	Type	Description	Default
force	bool	If True, recompute distances even when cached distances exist.	False
dist	str or None	Distance metric passed to scipy.spatial.distance.pdist. If None, self.metric is used.	None

Returns:

Name	Type	Description
distances	ndarray	Square sample-by-sample distance matrix.

to_adata(metadata: pd.DataFrame | None = None, *args, **kwargs) -> ad.AnnData

Convert the precomputed sample representation to an AnnData object.

Parameters:

Name	Type	Description	Default
metadata	DataFrame or None	Optional metadata to pass to the patpy conversion. If None, the metadata stored on the representation is used.	None
*args	tuple	Additional positional arguments passed to the parent method.	()
**kwargs	dict	Additional keyword arguments passed to the parent method.	{}

Returns:

Name	Type	Description
adata	AnnData	AnnData representation produced by the parent patpy method.