CyGroups: Cytoscape Groups

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

Cytoscape Groups

Description

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

Usage

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

## 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 Feb. 4, 2023, 5:12 p.m.