cospar.tmap.infer_Tmap_from_state_info_alone

cospar.tmap.infer_Tmap_from_state_info_alone(adata_orig, initial_time_points=None, later_time_point=None, initialize_method='OT', OT_epsilon=0.02, OT_dis_KNN=5, OT_cost='SPD', HighVar_gene_pctl=85, normalization_mode=1, sparsity_threshold=0.2, CoSpar_KNN=20, use_full_Smatrix=True, smooth_array=[15, 10, 5], trunca_threshold=[0.001, 0.01], compute_new=False, max_iter_N=[1, 5], epsilon_converge=[0.05, 0.05], use_fixed_clonesize_t1=False, sort_clone=1, save_subset=True, use_existing_KNN_graph=False)

Infer transition map from state information alone.

After initializing the clonal matrix as such that each cell has a unique barcode, it runs infer_Tmap_from_one_time_clones() to infer the transition map. Please see infer_Tmap_from_one_time_clones() for the meaning of each parameter.

Returns

• adata will include both the inferred transition map, and also the updated X_clone matrix.

• The input, adata_orig, will maintain the original X_clone matrix.