tangram.utils.project_cell_annotations
- tangram.utils.project_cell_annotations(adata_map, adata_sp, annotation='cell_type', threshold=0.5)
Transfer annotation from single cell data onto space.
- Parameters
adata_map (AnnData) – cell-by-spot AnnData returned by train function.
adata_sp (AnnData) – spatial data used to save the mapping result.
annotation (str) – Optional. Cell annotations matrix with shape (number_cells, number_annotations). Default is ‘cell_type’.
threshold (float) – Optional. Valid for using with adata_map.obs[‘F_out’] from ‘constrained’ mode mapping. Cell’s probability below this threshold will be dropped. Default is 0.5.
- Returns
None. Update spatial Anndata by creating obsm tangram_ct_pred field with a dataframe with spatial prediction for each annotation (number_spots, number_annotations)