CyGroups: Cytoscape Groups

Description Usage Arguments Details Value See Also Examples

Description

This function is used to create Cytoscape "groups" aspects.

Usage

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createCyGroups(
  id = NULL,
  name,
  nodes = NULL,
  externalEdges = NULL,
  internalEdges = NULL,
  collapsed = NULL
)

Arguments

id

integer (optional); Cytoscape group ids

name

character; names of the groups

nodes

list of integers (optional); reference to node ids

externalEdges

list of integers (optional); the external edges making up the group; reference to edge ids

internalEdges

list of integers (optional); the internal edges making up the group; reference to edge ids

collapsed

logical (optional); whether the group is displayed as a single node

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.

Cytoscape groups allow to group a set of Nodes and corresponding internal and external Edges together, and represent a group as a single node in the visualization. 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.

Value

CyGroupsAspect object

See Also

updateCyGroups;

Examples

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## a minimal example
cyGroups = createCyGroups(
  name = "Group One",
  nodes = list(c(1,2,3)),
  internalEdges = list(c(0,1))
)

## defining several groups at once
cyGroups = createCyGroups(
  name = c("Group One", "Group Two"),
  nodes = list(c(1,2,3), 0),
  internalEdges = list(c(0,1),NA)
)

## with all parameters
cyGroups = createCyGroups(
  id = c(0,1),
  name = c("Group One", "Group Two"),
  nodes = list(c(1,2,3), 0),
  internalEdges = list(c(0,1),NA),
  externalEdges = list(NA,c(1,3)),
  collapsed = c(TRUE,NA)                     
)

frankkramer-lab/RCX documentation built on July 14, 2021, 6:33 p.m.