CyVisualProperties: Cytoscape visual properties (aspect)

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

Cytoscape visual properties (aspect)

Description

This function is used to create Cytoscape visual properties aspects, that consists of CyVisualProperty objects for networks, nodes, edges, and default nodes and edges.

Usage

createCyVisualProperties(
  network = NULL,
  nodes = NULL,
  edges = NULL,
  defaultNodes = NULL,
  defaultEdges = NULL
)

Arguments

network	CyVisualProperty object (optional); the visual properties of networks
nodes	CyVisualProperty object (optional); the visual properties of nodes
edges	CyVisualProperty object (optional); the visual properties of edges
defaultNodes	CyVisualProperty object (optional); the default visual properties of nodes
defaultEdges	CyVisualProperty object (optional); the default visual properties of 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.

The visual properties aspect is the only aspect (CyVisualProperties) with a complex structure. It is composed of several sub-property classes and consists of CyVisualProperty objects, that belong to, or more precisely describe one of the following network elements: network, nodes, edges, defaultNodes or defaultEdges.

A single visual property (i.e. CyVisualProperty object) organizes the information as properties, dependencies and mappings, as well as the single values appliesTo and view, that define the subnetwork or view to which the IDs apply.

Properties are CyVisualPropertyProperties objects, that hold information like "NODE_FILL_COLOR" : "#26CCC9" or "NODE_LABEL_TRANSPARENCY" : "255" in a key-value like manner.

Dependencies are CyVisualPropertyDependencies objects, that hold information about dependencies between visual properties. Currently there are only three dependencies supported:

• Lock Node with and height: nodeSizeLocked = "false"

• Fit Custom Graphics to node: nodeCustomGraphicsSizeSync = "true"

• Edge color to arrows: arrowColorMatchesEdge = "false"

Mappings are CyVisualPropertyMappings objects, that hold information as a triplet consisting of name, type and definition, like "NODE_FILL_COLOR" : "DISCRETE" : "COL=molecule_type,T=string,K=0=miRNA,V=0=#FCEC00", "NODE_FILL_COLOR" : "CONTINUOUS" : "COL=gal1RGexp,T=double... or "NODE_LABEL" : "PASSTHROUGH" : "COL=COMMON,T=string".

For further information about Cytoscape visual properties see the Styles topic of the official Cytoscape documentation: http://manual.cytoscape.org/en/stable/Styles.html

Structure of Cytoscape Visual Properties

CyVisualProperties
|---network = CyVisualProperty
|---nodes = CyVisualProperty
|---edges = CyVisualProperty
|---defaultNodes = CyVisualProperty
|---defaultEdges = CyVisualProperty

CyVisualProperty
|---properties = CyVisualPropertyProperties
|   |--name
|   |--value 
|---dependencies = CyVisualPropertyDependencies
|   |--name
|   |--value 
|---mappings = CyVisualPropertyMappings
|   |--name
|   |--type
|   |--definition 
|---appliesTo = <reference to subnetwork id>
|---view = <reference to subnetwork id>

Value

CyVisualPropertiesAspect object

See Also

updateCyVisualProperties, updateCyVisualProperty, getCyVisualProperty

Examples

## Prepare used properties
## Visual property: Properties
vpPropertyP1 = createCyVisualPropertyProperties(c(NODE_BORDER_STROKE="SOLID"))

## Visual property: Dependencies
vpPropertyD1 = createCyVisualPropertyDependencies(c(nodeSizeLocked="false"))

## Visual property: Mappings
vpPropertyM1 = createCyVisualPropertyMappings(c(NODE_FILL_COLOR="CONTINUOUS"), 
                                              "COL=directed,T=boolean,K=0=true,V=0=ARROW")

## Create visual property object 
vpProperty1 = createCyVisualProperty(properties=vpPropertyP1, 
                                     dependencies=vpPropertyD1, 
                                     mappings=vpPropertyM1)

## Create a visual properties aspect
## (using the same visual property object for simplicity)
createCyVisualProperties(network=vpProperty1, 
                         nodes=vpProperty1, 
                         edges=vpProperty1, 
                         defaultNodes=vpProperty1, 
                         defaultEdges=vpProperty1)

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