spcoral.analysis.mapping_slides

spcoral.analysis.mapping_slides(adata_slide1, adata_slide2, n_merge=5, use_obsm='spatial')

Map expression profiles from one spatial slide onto the geometry of another slide via nearest-neighbor averaging.

Parameters:

• adata_slide1 (anndata.AnnData) – Target slide whose spatial coordinates will be used for the output. Spots in this object define the new grid positions.

• adata_slide2 (anndata.AnnData) – Source slide containing the expression/features to be transferred. Must have compatible spatial coordinates in obsm[use_obsm].

• n_merge (int, optional (default: 5)) – Number of nearest neighbors in adata_slide2 to average for each spot in adata_slide1.

• use_obsm (str, optional (default: 'spatial')) – Key in .obsm containing spatial coordinates (n_obs × 2 array).

Returns:

New AnnData object with: - .X: averaged expression matrix of shape (n_spots_slide1 × n_genes_slide2) - .obs: observation names from adata_slide1 - .var: variable (gene/feature) names from adata_slide2 - .obsm[use_obsm]: spatial coordinates copied from adata_slide1 Spots with no valid neighbors (extremely rare) are filtered out.

Return type:

anndata.AnnData