Create visualization of network — visualizeNetworks • MSstatsBioNet

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)

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

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.