diagrammer_format_signaling_graph: Prepare extracted ligand-target signaling network for...

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

Prepare extracted ligand-target signaling network for visualization with DiagrammeR.

Description

diagrammer_format_signaling_graph Prepare extracted ligand-target signaling network for visualization with DiagrammeR.

Usage

diagrammer_format_signaling_graph(signaling_graph_list, ligands_all,targets_all, sig_color = "steelblue", gr_color = "orange")

Arguments

signaling_graph_list	A list of two elements: sig: a data frame/ tibble containg weighted ligand-receptor and signaling interactions (from, to, weight); and gr: a data frame/tibble containng weighted gene regulatory interactions (from, to, weight)
ligands_all	A character vector of one or more ligands of interest
targets_all	A character vector of one or more target genes of interest
sig_color	The color for ligand-signaling edges and the ligand node. Default: steelblue.
gr_color	The color for the gene regulatory edges and the target node. Default: orange.

Value

A DiagrammeR Graph object ready for visualization via DiagrammeR::render_graph.

Examples

## Not run: 
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2",c("IL4","IL13"))
ligand_tf_matrix = construct_ligand_tf_matrix(weighted_networks, ligands, ltf_cutoff = 0.99, algorithm = "PPR", damping_factor = 0.5,ligands_as_cols = TRUE)
all_ligands = c("BMP2")
all_targets = c("HEY1")
top_n_regulators = 2
ligand_target_signaling_list = get_ligand_signaling_path(ligand_tf_matrix,all_ligands,all_targets,top_n_regulators,weighted_networks)
graph = diagrammer_format_signaling_graph(ligand_target_signaling_list, all_ligands,all_targets)
# DiagrammeR::render_graph(graph, layout = "tree")

## End(Not run)

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