createIgraphFromNetwork: Create an igraph network from a Cytoscape network

In cytoscape/RCy3: Functions to Access and Control Cytoscape

Create an igraph network from a Cytoscape network

Description

Takes a Cytoscape network and generates data frames for vertices and edges to send to the graph_from_data_frame function. Returns the network.suid and applies the perferred layout set in Cytoscape preferences.

Usage

createIgraphFromNetwork(network = NULL, base.url = .defaultBaseUrl)

Arguments

network	(optional) Name or SUID of the network. Default is the "current" network active in Cytoscape.
base.url	(optional) Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://localhost:1234 and the latest version of the CyREST API supported by this version of RCy3.

Details

Nodes and edges from the Cytoscape network will be translated into vertices and edges in igraph. Associated table columns will also be passed to igraph as vertiex and edge attributes. Note: all networks are implicitly modeled as directed in Cytoscape. Round-trip conversion of an undirected network in igraph via createNetworkFromIgraph to Cytoscape and back to igraph will result in a directed network.

Value

(igraph) an igraph network

See Also

createNetworkFromDataFrames, createNetworkFromIgraph

Examples

ig <- createIgraphFromNetwork()
ig <- createIgraphFromNetwork('myNetwork')

cytoscape/RCy3 documentation built on April 7, 2024, 2:17 p.m.