Create visualization of network

Use results from INDRA to generate a visualization of the a network on Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work.

Usage

visualizeNetworks(
  nodes,
  edges,
  pvalueCutoff = 0.05,
  logfcCutoff = 0.5,
  node_label_column = "id",
  main_targets = c()
)

Arguments

nodes

dataframe of nodes consisting of columns id (chararacter), pvalue (number), logFC (number)

edges

dataframe of edges consisting of columns source (character), target (character), interaction (character), evidenceCount (number), evidenceLink (character)

pvalueCutoff

p-value cutoff for coloring significant proteins. Default is 0.05

logfcCutoff

log fold change cutoff for coloring significant proteins. Default is 0.5

node_label_column

The column of the nodes dataframe to use as the node label. Default is "id". "hgncName" can be used for gene name.

main_targets

character vector of main targets to stand-out with a different node shape. Default is an empty vector c(). IDs of main targets should match the column used by the node_label_column parameter.

Value

cytoscape visualization of subnetwork

Examples

input <- data.table::fread(system.file(
    "extdata/groupComparisonModel.csv",
    package = "MSstatsBioNet"
))
subnetwork <- getSubnetworkFromIndra(input)
#> Warning: NOTICE: This function includes third-party software components
#>         that are licensed under the BSD 2-Clause License. Please ensure to
#>         include the third-party licensing agreements if redistributing this
#>         package or utilizing the results based on this package.
#>         See the LICENSE file for more details.
visualizeNetworks(subnetwork$nodes, subnetwork$edges)
#> Warning: Visualization is not available in non-interactive mode.