SPACEL.Splane.utils.add_cell_type_composition

SPACEL.Splane.utils.add_cell_type_composition(ad, prop_df=None, celltype_anno=None, all_celltypes=None)

Add cell type composition.

Adding cell type compostion to AnnData object of spatial transcriptomic data as Splane input.

Parameters:

  • ad – A AnnData object of spatial transcriptomic data as Splane input.

  • prop_df – A DataFrame of cell type composition used for spot-based spatial transcriptomic data.

  • celltype_anno – A list containing the cell type annotations for each cell in the single-cell resolution spatial transcriptomic data. This parameter is not used if prof_ad is provided.

  • all_celltypes – A list of all cell types present in all slices. This parameter is used when a single slice does not cover all cell types in the dataset.

Returns:

None