moscot.problems.space.AlignmentProblem.align

AlignmentProblem.align(reference=None, mode='warp', spatial_key=None, key_added=None)

Align the spatial data.

Parameters:

• reference (Optional[TypeVar(K, bound= Hashable)]) – Reference key. If a star policy was used, its reference will always be used.

• mode (Literal['warp', 'affine']) –

  Alignment mode. Valid options are:

  • 'warp' - warp the data to the reference.

  • 'affine' - align the data to the reference using affine transformation.

• spatial_key (Optional[str]) – Key in obsm where the spatial coordinates are stored. If None, use spatial_key.

• key_added (Optional[str]) – Key in obsm and uns where to store the alignment.

• self (SpatialAlignmentMixinProtocol[K, B]) –

Return type:

Optional[Tuple[ndarray[Any, dtype[float64]], Optional[Dict[TypeVar(K, bound= Hashable), Optional[ndarray[Any, dtype[float64]]]]]]]

Returns:

: Depending on the key_added:

• None - returns the aligned coordinates and metadata. The metadata is None when mode != 'affine'.

• str - updates adata with the following fields:

  • obsm['{key_added}'] - the aligned spatial coordinates.

  • uns['{key_added}']['alignment_metadata'] - the metadata.