Package index • COMMOTR

Core Analysis Functions

Main functions for spatial communication inference

spatial_communication(): Spatial Communication Inference

communication_direction(): Communication Direction Analysis

cluster_communication(): Cluster-Level Communication Analysis

cluster_communication_spatial_permutation(): Cluster communication with spatial permutation

COMMOTR-package COMMOTR: COMMOTR: Cell-Cell Communication via Collective Optimal Transport

Ligand-Receptor Database

Functions for loading and filtering LR databases

ligand_receptor_database(): Get ligand-receptor database

filter_lr_database(): Filter ligand-receptor database by expression

database_info: Built-in Ligand-Receptor Database Information

lr_database: Ligand-Receptor Database Functions

Downstream Analysis

Advanced analysis functions

communication_deg_detection(): Detect communication-dependent genes

communication_deg_clustering(): Cluster communication-dependent genes

communication_impact(): Analyze communication impact on gene expression

communication_spatial_autocorrelation(): Compute spatial autocorrelation of communication direction

group_cluster_communication(): Group cluster communications

group_cell_communication(): Group cell-cell communication patterns

group_communication_direction(): Group communication direction patterns

cluster_position(): Compute cluster centroid positions

downstream_analysis: Downstream Analysis Functions

Visualization

Plotting functions for results visualization

plot_cell_communication(): Plot cell-level communication

plot_cluster_communication(): Plot cluster-level communication network

plot_communication_dotplot(): Plot communication dotplot

plot_chord_diagram(): Plot chord diagram

plot_communication_heatmap(): Plot communication heatmap

plotting: Visualization Functions

Utilities

Helper functions for accessing results

get_communication_results(): Get COMMOTR results from Seurat object

get_communication_matrix(): Get communication matrix from results

get_sender_receiver_df(): Get sender/receiver summary data frame

print(<commotr_results>): Print method for COMMOTR results

summary(<commotr_results>): Summary method for COMMOTR results