API

preprocessing: pp

pp.spatial_mapping(ad_st, ad_sc, db[, ...])	Perform mapping of single-cell data to spatial transcriptomics data and spatial refinement.
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

tl.cell_shape_modeling(adata, cluster_key[, ...])	Perform cell shape modeling based on subcellular element method
tl.contact_communication(df_ligrec, adata[, ...])	Contact-base communication inference
tl.cluster_communication(adata, cluster_key, ...)	Summarize cell-cell communication to cluster-cluster communication and compute p-values by permutating cell/spot labels.

plotting: pl

pl.plot_cell_shape(sem[, vis_key, arr, ...])	Plot cell shape using alpha shape, visualize cell data by colors.
pl.plot_contact_signal([sem, adata, ...])	Visualize contact signals or relationships between cells