stlearn.spatial.SME.SME_impute0

stlearn.spatial.SME.SME_impute0(adata: anndata._core.anndata.AnnData, use_data: str = 'raw', weights: Literal[weights_matrix_all, weights_matrix_pd_gd, weights_matrix_pd_md, weights_matrix_gd_md, gene_expression_correlation, physical_distance, morphological_distance] = 'weights_matrix_all', platform: Literal[Visium, Old_ST] = 'Visium', copy: bool = False) → Optional[anndata._core.anndata.AnnData]

using spatial location (S), tissue morphological feature (M) and gene expression (E) information to impute missing values

Parameters

• adata – Annotated data matrix.

• use_data – input data, can be raw counts or log transformed data

• weights – weighting matrix for imputation. if weights_matrix_all, matrix combined all information from spatial location (S), tissue morphological feature (M) and gene expression (E) if weights_matrix_pd_md, matrix combined information from spatial location (S), tissue morphological feature (M)

• platform – Visium or Old_ST

• copy – Return a copy instead of writing to adata.

Returns

Return type

Anndata