commot.pp.ligand_receptor_database
- commot.pp.ligand_receptor_database(database='CellChat', species='mouse', heteromeric_delimiter='_', signaling_type='Secreted Signaling')
Extract ligand-receptor pairs from LR database.
- Parameters
database – The name of the ligand-receptor database. Currently, only CellChatDB [Jin2021] is available.
species – The species of the ligand-receptor pairs. Choose between ‘mouse’ and ‘human’.
heteromeric_delimiter – The character to separate the heteromeric units of heteromeric ligands and receptors. For example, if the heteromeric receptor (TGFbR1, TGFbR2) will be represented as ‘TGFbR1_TGFbR2’ if this parameter is set to ‘_’.
signaling_type – The type of signaling. Choose from ‘Secreted Signaling’, ‘Cell-Cell contact’, and ‘ECM-Receptor’. If None, all pairs in the database are returned.
- Returns
df_ligrec – A pandas DataFrame of the LR pairs with the three columns representing the ligand, receptor, and the signaling pathway name, respectively.
- Return type
pandas.DataFrame
References
- Jin2021
Jin, S., Guerrero-Juarez, C. F., Zhang, L., Chang, I., Ramos, R., Kuan, C. H., … & Nie, Q. (2021). Inference and analysis of cell-cell communication using CellChat. Nature communications, 12(1), 1-20.