CySubNetworks: Cytoscape subnetworks

In frankkramer-lab/RCX: R package implementing the Cytoscape Exchange (CX) format

Cytoscape subnetworks

Description

This function is used to create Cytoscape subnetwork aspects.

Usage

createCySubNetworks(id, nodes = NULL, edges = NULL)

Arguments

id	integer; subnetwork IDs
nodes	integer; reference to node id OR character "all" to refer to all nodes
edges	integer; reference to edge id OR character "all" to refer to all edges

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

A group is defined by its unique id, which must be an (positive) integer, which serves as reference to other aspects. If no IDs are provided, they are created automatically.

Nodes and edges are referred by the IDs of the corresponding aspect. Unlike other aspects referring those IDs, the Cytoscape subnetwork aspect allows to refer to all nodes and edges using the keyword all.

The relationship between (sub-)networks and views, and also the type (subnetwork or view) is defined in CyNetworkRelations.

Value

CySubNetworksAspect object

See Also

updateCySubNetworks;

Examples

## a minimal example
cySubNetworks = createCySubNetworks(
  nodes = "all",
  edges = "all"
)

## defining several subnetworks at once
cySubNetworks = createCySubNetworks(
  nodes = list("all",
               c(1,2,3)),
  edges = list("all",
               c(0,2))
)

## with all parameters
cySubNetworks = createCySubNetworks(
  id = c(0,1),
  nodes = list("all",
               c(1,2,3)),
  edges = list("all",
               c(0,2))                    
)

frankkramer-lab/RCX documentation built on Feb. 4, 2023, 5:12 p.m.