OmicVerse Single-Cell CellPhoneDB Communication

Goal

Run the reusable CellPhoneDB communication spine on single-cell AnnData: verify the expression matrix and cell-type annotations, run ov.single.run_cellphonedb_v5(...), convert the results into the visualization-ready interaction AnnData, then optionally continue into aggregated network plots, pathway summaries, ligand-receptor contribution views, bubble plots, chord diagrams, and signaling-role analysis through ov.pl.CellChatViz(...). Keep the skill centered on one processed CellPhoneDB result object rather than on the tutorial dataset.

Quick Workflow

1. Inspect the input AnnData, especially the cell-type column, gene-symbol convention, and whether the matrix looks compatible with CellPhoneDB.
2. Ensure the CellPhoneDB database archive is available or let the wrapper download it automatically.
3. Run ov.single.run_cellphonedb_v5(...) with explicit filtering, permutation, and output settings.
4. Treat the returned cpdb_results dict and adata_cpdb object as the shared handoff point for all downstream visualization branches.
5. Initialize viz = ov.pl.CellChatViz(adata_cpdb, palette=...).
6. Choose the downstream branch the user actually asked for: aggregated network, pathway-level aggregation, ligand-receptor extraction, bubble/chord views, or signaling-role analysis.
7. Validate the expected layers, sender/receiver annotations, and pathway metadata before trusting any plot.

Interface Summary