CyVisualPropertyMappings: Create an object for mappings of Cytoscape Visual Properties...

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

Create an object for mappings of Cytoscape Visual Properties (object used in CyVisualProperty)

Description

This function is used to create objects for mappings in Cytoscape visual properties. Networks, nodes, edges, and default nodes and edges mappings are realized as CyVisualProperty objects, that each consist of properties (CyVisualPropertyProperties objects), dependencies (CyVisualPropertyDependencies objects) and mappings (this here).

Usage

createCyVisualPropertyMappings(type, definition, name = NULL)

Arguments

type	character or named character; value of the mappings
definition	character; definitions of the mappings
name	character (optional); names of the mappings

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

CyVisualPropertyMappings object

Note

If name is not provided, the names(type) is used instead to infer the names.

See Also

updateCyVisualProperty, updateCyVisualProperties

Examples

## Using a named vector
vpMappingNamedType = c(NODE_FILL_COLOR="CONTINUOUS",
                       EDGE_TARGET_ARROW_SHAPE="DISCRETE")
vpMappingDefinition = c("COL=gal1RGexp,T=double,...",
                        "COL=directed,T=boolean,K=0=true,V=0=ARROW")
createCyVisualPropertyMappings(vpMappingNamedType, 
                               vpMappingDefinition)

## Using three separate vectors
vpMappingName = c("NODE_FILL_COLOR", 
                  "EDGE_TARGET_ARROW_SHAPE")
vpMappingType = c("CONTINUOUS", 
                  "DISCRETE")
createCyVisualPropertyMappings(vpMappingType, 
                               vpMappingDefinition, 
                               vpMappingName)

# Result for either:
#                      name       type                                definition
# 1         NODE_FILL_COLOR CONTINUOUS                COL=gal1RGexp,T=double,...
# 2 EDGE_TARGET_ARROW_SHAPE   DISCRETE COL=directed,T=boolean,K=0=true,V=0=ARROW

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