pyXenium.cci.cci_topology_analysis#

cci_topology_analysis(*, reference_df=None, expression_df=None, interaction_pairs, output_dir=None, adata=None, entity_points_df=None, tbc_results=None, t_and_c_df=None, cluster_col='cluster', cell_id_col='cell_id', x_col='x', y_col='y', celltype_col='celltype', ligand_col='ligand', receptor_col='receptor', prior_col='evidence_weight', structure_map=None, structure_map_df=None, anchor_mode='precomputed', expression_support_mode='pseudobulk_detection', contact_mode='strength_coverage', entity_min_weight=0.0, detection_threshold=0.0, k_neighbors=8, radius=None, topology_method='average', top_n_pairs=12, hotspot_quantile=0.9, min_cross_edges=50, contact_expr_threshold='q75_nonzero', null_model='none', n_permutations=100, random_state=0, interaction_mode_col='interaction_mode', distance_kernel='contact', downstream_targets=None, return_hotspots=True, export_figures=True, use_raw=False)#

Score cell-cell interaction hypotheses using topology anchors, sender/receiver expression support, and de-saturated local contact structure.

Parameters:

  • reference_df (DataFrame | None)

  • expression_df (DataFrame | None)

  • interaction_pairs (DataFrame)

  • output_dir (str | Path | None)

  • adata (Any)

  • entity_points_df (DataFrame | None)

  • tbc_results (str | Path | None)

  • t_and_c_df (DataFrame | None)

  • cluster_col (str)

  • cell_id_col (str)

  • x_col (str)

  • y_col (str)

  • celltype_col (str)

  • ligand_col (str)

  • receptor_col (str)

  • prior_col (str)

  • structure_map (DataFrame | None)

  • structure_map_df (DataFrame | None)

  • anchor_mode (str)

  • expression_support_mode (str)

  • contact_mode (str)

  • entity_min_weight (float)

  • detection_threshold (float)

  • k_neighbors (int)

  • radius (float | None)

  • topology_method (str)

  • top_n_pairs (int)

  • hotspot_quantile (float)

  • min_cross_edges (int)

  • contact_expr_threshold (str | float)

  • null_model (str)

  • n_permutations (int)

  • random_state (int | None)

  • interaction_mode_col (str | None)

  • distance_kernel (str)

  • downstream_targets (Mapping[str, Sequence[str]] | DataFrame | None)

  • return_hotspots (bool)

  • export_figures (bool)

  • use_raw (bool)

Return type:

dict[str, Any]