Index A | B | C | F | G | L | M | N | P | R | S | T A apply_cutoff_labels() (in module cytogater) assign_confident_labels() (in module cytogater) assign_soft_labels() (in module cytogater) B build_fullcoverage_tree() (in module cytogater) build_hierarchical_reference() (in module cytogater) build_lineage_hierarchy() (in module cytogater) C calculate_f1() (in module cytogater) calculate_soft_scores() (in module cytogater) calculate_spatial_prior_labels() (in module cytogater) calculate_uncertainty() (in module cytogater) class_metrics_from_fit() (in module cytogater) collect_path_scores() (in module cytogater) compute_custom_labels() (in module cytogater) custom_labels() (in module cytogater) F fit_gmm_2() (in module cytogater) fit_marker_stats() (in module cytogater) G gmm_equal_posterior_cutoff() (in module cytogater) L label_agreement_rates() (in module cytogater) label_confusion_matrix() (in module cytogater) M marker_separability() (in module cytogater) N neg_penalty() (in module cytogater) P plot_celltype_tree() (in module cytogater) plot_class_metrics() (in module cytogater) plot_confusion_matrix() (in module cytogater) plot_ct_marker_intensity() (in module cytogater) plot_label_agreement() (in module cytogater) plot_label_cardinality() (in module cytogater) plot_label_confusion_matrix() (in module cytogater) plot_label_counts() (in module cytogater) plot_label_dotplot() (in module cytogater) plot_labelled_cells() (in module cytogater) plot_marker_density() (in module cytogater) plot_marker_priority_tree() (in module cytogater) plot_probability_map() (in module cytogater) plot_pseudobulk_heatmap() (in module cytogater) plot_rand_cell_probs() (in module cytogater) plot_score_hist() (in module cytogater) predict_hierarchical_knn_recursive() (in module cytogater) predict_unknown_with_dl() (in module cytogater) predict_unknown_with_knn() (in module cytogater) predict_unknown_with_randomforest() (in module cytogater) predict_wknn_multi() (in module cytogater) print_celltype_tree() (in module cytogater) prob_mad_cutoff() (in module cytogater) prob_quantile_cutoff() (in module cytogater) probability_label_matrix() (in module cytogater) R rf_metric_table() (in module cytogater) rf_metric_text() (in module cytogater) run_soft_gating() (in module cytogater) run_tree_gating() (in module cytogater) S score_marker_logistic() (in module cytogater) score_marker_rank() (in module cytogater) T train_custom_dl() (in module cytogater) train_custom_knn() (in module cytogater) train_custom_randomforest() (in module cytogater) tree_prob() (in module cytogater) tree_to_df() (in module cytogater)