createSubnetwork: Create subnetwork from existing network

In cytoscape/RCy3: Functions to Access and Control Cytoscape

Create subnetwork from existing network

Description

Copies a subset of nodes and edges into a newly created subnetwork.

Usage

createSubnetwork(
  nodes = NULL,
  nodes.by.col = "SUID",
  edges = NULL,
  edges.by.col = "SUID",
  exclude.edges = FALSE,
  subnetwork.name = NULL,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

nodes	list of nodes by SUID, by specified nodes.by.col value (e.g., name) or by keyword: selected, unselected or all. Default is currently selected nodes.
nodes.by.col	name of node table column corresponding to provided nodes list; default is 'SUID'
edges	list of edges by SUID, by specified nodes.by.col value (e.g., name) or by keyword: selected, unselected or all. Default is currently selected edges.
edges.by.col	name of edge table column corresponding to provided edges list; default is 'SUID'
exclude.edges	(boolean) whether to exclude connecting edges; default is FALSE
subnetwork.name	name of new subnetwork to be created; default is to add a numbered suffix to source network name
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

If you specify both nodes and edges, the resulting subset will be the union of those sets. Typical usage only requires specifying either nodes or edges. Note that selected nodes will bring along their connecting edges by default (see exclude.edges arg) and selected edges will always bring along their source and target nodes.

Value

SUID of new subnetwork

Examples

createSubnetwork()
createSubnetwork("all")
createSubnetwork(subnetwork.name="mySubnetwork")
createSubnetwork(c("node 1","node 2","node 3"),"name")
createSubnetwork(c("AKT1","TP53","PIK3CA"),"display name")
createSubnetwork(edges="all") #subnetwork of all connected nodes

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