spateo.alignment.paste_alignment¶
Functions¶
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Align spatial coordinates of models. |
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Align the spatial coordinates of one model list through the affine transformation matrix obtained from another model list. |
Module Contents¶
- spateo.alignment.paste_alignment.paste_align(models: List[anndata.AnnData], layer: str = 'X', genes: list | numpy.ndarray | None = None, spatial_key: str = 'spatial', key_added: str = 'align_spatial', mapping_key_added: str = 'models_align', alpha: float = 0.1, numItermax: int = 200, numItermaxEmd: int = 100000, dtype: str = 'float64', device: str = 'cpu', verbose: bool = True, **kwargs) Tuple[List[anndata.AnnData], List[numpy.ndarray | numpy.ndarray]] [source]¶
Align spatial coordinates of models.
- Parameters:
- models
List of models (AnnData Object).
- layer
If
'X'
, uses.X
to calculate dissimilarity between spots, otherwise uses the representation given by.layers[layer]
.- genes
Genes used for calculation. If None, use all common genes for calculation.
- spatial_key
The key in
.obsm
that corresponds to the raw spatial coordinate.- key_added
.obsm
key under which to add the aligned spatial coordinates.- mapping_key_added
.uns key under which to add the alignment info.
- alpha
Alignment tuning parameter. Note: 0 <= alpha <= 1.
When
alpha = 0
only the gene expression data is taken into account, while whenalpha =1
only the spatial coordinates are taken into account.- numItermax
Max number of iterations for cg during FGW-OT.
- numItermaxEmd
Max number of iterations for emd during FGW-OT.
- dtype
The floating-point number type. Only
float32
andfloat64
.- device
Equipment used to run the program. You can also set the specified GPU for running.
E.g.: '0'
.- verbose
If
True
, print progress updates.- **kwargs
Additional parameters that will be passed to
pairwise_align
function.
- Returns:
List of models (AnnData Object) after alignment. pis: List of pi matrices.
- Return type:
align_models
- spateo.alignment.paste_alignment.paste_align_ref(models: List[anndata.AnnData], models_ref: List[anndata.AnnData] | None = None, n_sampling: int | None = 2000, sampling_method: str = 'trn', layer: str = 'X', genes: list | numpy.ndarray | None = None, spatial_key: str = 'spatial', key_added: str = 'align_spatial', mapping_key_added: str = 'models_align', alpha: float = 0.1, numItermax: int = 200, numItermaxEmd: int = 100000, dtype: str = 'float64', device: str = 'cpu', verbose: bool = True, **kwargs) Tuple[List[anndata.AnnData], List[anndata.AnnData], List[numpy.ndarray | numpy.ndarray]] [source]¶
Align the spatial coordinates of one model list through the affine transformation matrix obtained from another model list.
- Parameters:
- models
List of models (AnnData Object).
- models_ref
Another list of models (AnnData Object).
- n_sampling
When
models_ref
is None, new data containing n_sampling coordinate points will be automatically generated for alignment.- sampling_method
The method to sample data points, can be one of
["trn", "kmeans", "random"]
.- layer
If
'X'
, uses.X
to calculate dissimilarity between spots, otherwise uses the representation given by.layers[layer]
.- genes
Genes used for calculation. If None, use all common genes for calculation.
- spatial_key
The key in
.obsm
that corresponds to the raw spatial coordinates.- key_added
.obsm
key under which to add the aligned spatial coordinates.- mapping_key_added
.uns key under which to add the alignment info.
- alpha
Alignment tuning parameter. Note: 0 <= alpha <= 1.
When
alpha = 0
only the gene expression data is taken into account, while whenalpha =1
only the spatial coordinates are taken into account.- numItermax
Max number of iterations for cg during FGW-OT.
- numItermaxEmd
Max number of iterations for emd during FGW-OT.
- dtype
The floating-point number type. Only
float32
andfloat64
.- device
Equipment used to run the program. You can also set the specified GPU for running.
E.g.: '0'
.- verbose
If
True
, print progress updates.- **kwargs
Additional parameters that will be passed to
models_align
function.
- Returns:
List of models (AnnData Object) after alignment. align_models_ref: List of models_ref (AnnData Object) after alignment. pis: The list of pi matrices from align_models_ref.
- Return type:
align_models