| display_node_neighboorhood {cosmosR} | R Documentation |
display input and measurements within n steps of a given set of nodes
display_node_neighboorhood(central_node, sif, att, n = 100)
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, as returned by the format_cosmos_res function |
att |
df; attributes of the nodes of the COMSOS network solution, as returned by the format_cosmos_res function |
n |
numeric; maximum number of steps in the network to look for inputs and measurments |
a visnetwork object
CARNIVAL_options <- cosmosR::default_CARNIVAL_options()
CARNIVAL_options$solver <- "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)
data(metabolite_to_pubchem)
data(omnipath_ptm)
test_result_for <- format_COSMOS_res(test_result_for,
metab_mapping = metabolite_to_pubchem,
measured_nodes = unique(c(names(toy_metabolic_input),
names(toy_signaling_input))),
omnipath_ptm = omnipath_ptm)
network_plot <- display_node_neighboorhood(central_node = 'BCAT1',
sif = test_result_for[[1]],
att = test_result_for[[2]],
n = 5)
network_plot