getCyVisualProperty: Get a Cytoscape visual property (object used in...

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

Get a Cytoscape visual property (object used in CyVisualProperties aspect) by appliesTo and view

Description

This function helps filtering CyVisualProperty objects by appliesTo and view attributes (i.e. a unique combination of both). If nothing matches the searched pattern NULL is returned.

Usage

getCyVisualProperty(cyVisualProperty, appliesTo = NA, view = NA)

Arguments

cyVisualProperty	CyVisualProperty object
appliesTo	integer (optional); value of appliesTo to filter for
view	integer (optional); value of view to filter for

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

CyVisualProperty object containing only one element, or NULL

See Also

updateCyVisualProperty, updateCyVisualProperties

Examples

## 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 
vpProperty = createCyVisualProperty(properties=list(vpPropertyP1,
                                                    vpPropertyP1,
                                                    vpPropertyP1), 
                                    dependencies=list(vpPropertyD1,
                                                      vpPropertyD1,
                                                      NA), 
                                    mappings=list(vpPropertyM1,
                                                  NA,
                                                  vpPropertyM1),
                                    appliesTo = c(NA,
                                                  NA,
                                                  1),
                                    view = c(NA,
                                             1,
                                             1))

## Get VP for no subnetwork an no view
getCyVisualProperty(vpProperty)

getCyVisualProperty(vpProperty, 
                    appliesTo = 1,
                    view = 1)

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