Single-cell CellPhoneDB communication mapping

Overview

Apply this skill when a user wants to quantify ligand-receptor communication between annotated single-cell populations and visualize the result with OmicVerse's CellPhoneDB plotting stack. This skill now covers both the original low-level ov.pl.CellChatViz workflow and the newer public plotting APIs:

• ov.pl.ccc_heatmap(...)
• ov.pl.ccc_network_plot(...)
• ov.pl.ccc_stat_plot(...)

Use the ccc_* functions by default when the goal is to quickly generate publication-ready plots with a stable public API. Drop down to CellChatViz when the user needs method-level control or wants to combine several custom visualizations in one notebook.

Instructions

1. Prepare the environment
   • Use an environment with omicverse>=0.2, scanpy, anndata, pandas, matplotlib, seaborn, and CellPhoneDB resources.
   • For the newer visualizations, also ensure these optional plotting dependencies are available when needed:
     • marsilea for heatmap and bubble matrix plotters.
     • mpl-chord-diagram for chord diagrams.
     • networkx for diffusion and network-style plots.
     • adjustText if the user wants improved automatic label repulsion.