Use customed pathways

Create pathways_custom

Please follow the structure and colnames of pathways or demo_pathways() as follows:

# pathways is a data.frame object with 8 columns

src	dest	pathway	source	type	src_tf	dest_tf	species
CDKN1A	CDK2	p53 signaling pathway	KEGG	Process(activation)	NO	NO	Human
CDKN1A	CDK4	p53 signaling pathway	KEGG	Process(activation)	NO	NO	Human
CDK2	TP53	p53 signaling pathway	KEGG	Process(binding)	NO	YES	Human
Akt1	Atf2	PI3K-Akt signaling pathway	KEGG	Process(association)	NO	YES	Mouse

Note: dest_tf means dest is a transcriptional factor (TF), e.g., TP53, Atf2

Use pathways_custom

Replace the pathways with pathways_custom in the function of find_lr_path() to infer cell-cell communications

find_lr_path(object, lrpairs, pathways = pathways_custom, max_hop)