single-cell-cellphonedb-communication-mapping

Key Notes

• Apply this skill when a user wants to quantify ligand–receptor communication between annotated single-cell populations and display the networks with CellChatViz. It distils the workflow from t_cellphonedb.ipynb, which analyses EVT trophoblast data.
• Use an environment with omicverse>=0.2, scanpy, anndata, pandas, matplotlib, and cellphonedb resources. The tutorial assumes the pre-built CellPhoneDB v5 SQLite bundle downloaded as cellphonedb.zip in the working directory.
• Activate omicverse plotting defaults via ov.plot_set() so that downstream figures follow the project palette.
• Read the normalised counts with adata = ov.read('data/cpdb/normalised_log_counts.h5ad').
• Filter to the cell populations of interest using adata.obs['cell_labels'] (e.g., EVT, dNK, VCT). Ensure adata.obs['cell_labels'] is categorical and free of missing values so CellPhoneDB groups cells correctly.