cellina.compute_spatial_features

cellina.compute_spatial_features(adata, connectivity_key='spatial_connectivities', neighbor_genes=None, obsm_key='spatial_x', layer=None)

Compute spatial neighbourhood features and store them in adata.obsm. Expects normalized counts in adata.X (or adata.layers[layer]) and a spatial connectivity matrix in adata.obsp[connectivity_key].

Parameters:

• adata (AnnData) – AnnData object.

• connectivity_key (str (default: 'spatial_connectivities')) – Key in adata.obsp for the spatial connectivity matrix.

• neighbor_genes (Optional[List[str]] (default: None)) – Subset of genes to aggregate. None means all genes.

• obsm_key (str (default: 'spatial_x')) – Key in adata.obsm where the result is stored.

• layer (Optional[str] (default: None)) – Key in adata.layers to use as expression source. When None, adata.X is used.

Return type:

None