prepare_ligand_target_visualization: Prepare heatmap visualization of the ligand-target links...

In saeyslab/nichenetr: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

Prepare heatmap visualization of the ligand-target links starting from a ligand-target tibble.

Description

prepare_ligand_target_visualization Prepare heatmap visualization of the ligand-target links starting from a ligand-target tibble. Get regulatory potential scores between all pairs of ligands and targets documented in this tibble. For better visualization, we propose to define a quantile cutoff on the ligand-target scores.

Usage

prepare_ligand_target_visualization(ligand_target_df, ligand_target_matrix, cutoff = 0.25)

Arguments

ligand_target_df	Tibble with columns 'ligand', 'target' and 'weight' to indicate ligand-target regulatory potential scores of interest.
ligand_target_matrix	The NicheNet ligand-target matrix denoting regulatory potential scores between ligands and targets (ligands in columns).
cutoff	Quantile cutoff on the ligand-target scores of the input weighted ligand-target network. Scores under this cutoff will be set to 0.

Value

A matrix giving the ligand-target regulatory potential scores between ligands of interest and their targets genes part of the gene set of interest.

Examples

## Not run: 
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2","IL4")
ligand_target_matrix = construct_ligand_target_matrix(weighted_networks, ligands, ltf_cutoff = 0, algorithm = "PPR", damping_factor = 0.5, secondary_targets = FALSE)
geneset = c("SOCS2","SOCS3", "IRF1")
background_expressed_genes = c("SOCS2","SOCS3","IRF1","ICAM1","ID1","ID2","ID3")
active_ligand_target_links_df = potential_ligands %>% lapply(get_weighted_ligand_target_links, geneset = geneset, ligand_target_matrix = ligand_target_matrix, n = 250) %>% bind_rows()
active_ligand_target_links = prepare_ligand_target_visualization(ligand_target_df = active_ligand_target_links_df, ligand_target_matrix = ligand_target_matrix, cutoff = 0.25)

## End(Not run)

saeyslab/nichenetr documentation built on March 26, 2024, 9:22 a.m.