nichesphere.comm.lr_ctPairScores_perCat_dir

nichesphere.comm.lr_ctPairScores_perCat_dir#

nichesphere.comm.lr_ctPairScores_perCat_dir(ccommTable, db, dbCatCol, dbMatchCol, ccommMatchCol, ccommLRscoresCol, oneCTinteractions, condition, pairCatDF)#

Calculate cell communication scores per ligand category from a database

Parameters:

  • ccommTable (pd.DataFrame) – Condition specific cell - cell communication table (output from CrossTalkeR)

  • db (pd.DataFrame) – database table with information about element (ligand or receptor or both) category (eg: biological processes)

  • dbCatCol (str) – column in the database table containing the category (eg: biological process) with which the ligands/receptors/LR pairs are associated

  • dbMatchCol (str) – column in the database table containing the elements (ligands/receptors/LR pairs) associated to the categories

  • ccommMatchCol (str) – column in the ccommTable table containing the elements (ligands/receptors/LR pairs) associated to the categories

  • ccommLRscoresCol (str) – name of the ccommTable column where the LR scores are (usually ‘MeanLR’ for CrossTalkeR)

  • oneCTinteractions (list) – list of single cell interactions (celltype@celltype)

  • condition (str) – name of the analyzed condition (a column with this string will be added to the resulting table)

  • pairCatDF (pd.DataFrame) – dataframe of cell pairs and corresponding co-localization niche pairs

Returns:

CTpairScores_byCat – cell communication table with new columns ‘cell_pairs’, ‘niche_pairs’, ‘LRcat’ and ‘condition’

Return type:

pd.DataFrame