nichenetr (version 0.1.0)

prepare_ligand_target_visualization: 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)
 = c("TNF","BMP2","IL4")
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)
# }
# NOT RUN {
# }