display_node_neighboorhood: display_node_neighboorhood

In saezlab/COSMOS: COSMOS (Causal Oriented Search of Multi-Omic Space)

display_node_neighboorhood

Description

display input and measurements within n steps of a given set of nodes

Usage

display_node_neighboorhood(central_node, sif, att, n = 100)

Arguments

central_node	character or character vector; node ID(s) around which a network will be branched out untill meansurments and input are reached
sif	df; COSMOS network solution in sif format like the first list element returned by the format_cosmos_res function
att	df; attributes of the nodes of the COMSOS network solution like the second list element returned by the format_cosmos_res function
n	numeric; maximum number of steps in the network to look for inputs and measurments

Value

a visnetwork object

Examples

CARNIVAL_options <- cosmosR::default_CARNIVAL_options("lpSolve")
data(toy_network)
data(toy_signaling_input)
data(toy_metabolic_input)
data(toy_RNA)
test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network,
signaling_data = toy_signaling_input,
metabolic_data = toy_metabolic_input,
diff_expression_data = toy_RNA,
maximum_network_depth = 15,
remove_unexpressed_nodes = TRUE,
CARNIVAL_options = CARNIVAL_options
)
test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for,
CARNIVAL_options = CARNIVAL_options)
test_result_for <- format_COSMOS_res(test_result_for)
network_plot <- display_node_neighboorhood(central_node = 'MYC',
sif = test_result_for[[1]],
att = test_result_for[[2]],
n = 7)
network_plot

saezlab/COSMOS documentation built on Sept. 17, 2023, 1:22 p.m.