destvi_utils.explore_gamma_space
- destvi_utils.explore_gamma_space(st_model, sc_model, st_adata=None, ct_thresholds=None, output_file=None, ct_list=None, key_proportions='proportions', key_spatial='spatial')[source]
Function to compute automatic threshold on cell type proportion values. For further reference check [Lopez22].
- Parameters
- st_model
Trained destVI model
- sc_model
Trained CondSCVI model
- st_adata
Spatial sequencing dataset with proportions in obsm[key_proportions]. Otherwise uses data in st_model.
- ct_threshold
List with threshold values for cell type proportions
- output_file
File where html output is stored. None means displaying the results and not storing them. Defaults to None.
- ct_list
Celltypes to use. Defaults to all celltypes.
- key_proportions
Obsm key pointing to cell-type proportions.
- key_spatial
Obsm key pointing to location of cells.