HoloNet.preprocessing.get_expressed_lr_df#
- HoloNet.preprocessing.get_expressed_lr_df(interaction_db, complex_db, adata, expressed_prop=0.15)#
Filter the dataframe with pairwise ligand and receptor gene, requiring ligand and receptor genes to be expressed in a certain percentage of cells (or spots). And generate the ‘LR_pair’ column as the used names of ligand–receptor pairs in following workflow.
- Parameters
- interaction_db
from cellchatDB
- complex_db
from cellchatDB
- adata
Annotated data matrix.
- expressed_prop default:
0.15 The percentage of cells required to express ligand and receptor genes in at least.
- Returns
: A preprocessed LR-gene dataframe.