API

Preprocessing: pp

pp.infer_spatial_information(adata_sc, adata_sp)	Infer spatial information.
pp.ligand_receptor_database([database, ...])	Extract ligand-receptor pairs from LR database.
pp.filter_lr_database(df_ligrec, adata[, ...])	Filter ligand-receptor pairs.

Tools: tl

Communication inference

tl.spatial_communication(adata[, ...])	Infer spatial communication.
tl.communication_direction(adata[, ...])	Construct spatial vector fields for inferred communication.
tl.cluster_communication(adata[, ...])	Summarize cell-cell communication to cluster-cluster communication and compute p-values by permutating cell/spot labels.
tl.cluster_communication_spatial_permutation(adata)	Infer cluster-cluster communication and compute p-value by permutating cell/spot locations.
tl.cluster_position(adata[, clustering, ...])	Assign spatial positions to clusters.

Downstream analysis

tl.communication_deg_detection(adata[, ...])	Identify signaling dependent genes
tl.communication_deg_clustering(df_deg, df_yhat)	Cluster the communcation DE genes based on their fitted expression pattern.
tl.communication_impact(adata[, ...])	Analyze impact of communication.
tl.group_cluster_communication(adata[, ...])	Idenfitify groups of cluster-cluster communication with similar pattern.
tl.group_cell_communication(adata[, keys, ...])	Idenfitify groups of cell-cell communication with similar pattern.
tl.group_communication_direction(adata[, ...])	Idenfitify groups of communication directions with similar pattern.
tl.communication_spatial_autocorrelation(adata)	Spatial autocorrelation of communication directions.

Plotting: pl

pl.plot_cell_communication(adata[, ...])	Plot spatial directions of cell-cell communication.
pl.plot_cluster_communication_network(adata)	Plot cluster-cluster communication as network.
pl.plot_cluster_communication_dotplot(adata)	Plot cluster-cluster communication through multiple ligand-receptor pairs as dotplot.
pl.plot_communication_dependent_genes(...[, ...])	Plot smoothed gene expression of the detected communication-dependent genes.
pl.plot_communication_impact(df_impact[, ...])	Plot communication impact obtained by running the function commot.tl.communication_impact().