display_node_neighboorhood {cosmosR} | R Documentation

## 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()
    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 = 'NFKB1',
    sif = test_result_for[[1]],
    att = test_result_for[[2]],
    n = 7)
    network_plot

[Package cosmosR version 1.2.0 Index]