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

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

if (FALSE) { # \dontrun{
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, lr_network, 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")
} # }