updateCyVisualProperty: Update Cytoscape Visual Property objects and sub-objects...

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

Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect)

Description

This function is used to add Cytoscape visual property objects (CyVisualProperty) and its sub-objects (CyVisualPropertyProperties, CyVisualPropertyDependencies and CyVisualPropertyMappings) to each other. Cytoscape visual property objects define networks, nodes, edges, and default nodes and edges in a CyVisualProperties aspect.

Usage

updateCyVisualProperty(
  cyVisualProperty,
  additionalProperty,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  .log = c()
)

## S3 method for class 'CyVisualPropertyProperties'
updateCyVisualProperty(
  cyVisualProperty,
  additionalProperty,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  .log = c()
)

## S3 method for class 'CyVisualPropertyDependencies'
updateCyVisualProperty(
  cyVisualProperty,
  additionalProperty,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  .log = c()
)

## S3 method for class 'CyVisualPropertyMappings'
updateCyVisualProperty(
  cyVisualProperty,
  additionalProperty,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  .log = c()
)

## S3 method for class 'CyVisualProperty'
updateCyVisualProperty(
  cyVisualProperty,
  additionalProperty,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  .log = c()
)

Arguments

cyVisualProperty	object; (to which it will be added)
additionalProperty	object; (that will be added)
replace	logical; if existing values are updated (or ignored)
stopOnDuplicates	logical; whether to stop, if duplicates in name (and subnetworkId if present) column are found
.log	character (optional); name of the calling function used in error logging

Details

Structure of Cytoscape Visual Property

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

CyVisualProperty objects differ in the sub-networks and views (CySubNetworks) they apply to, subsequently properties, dependencies and mappings are merged based on the uniqueness in those two.

Properties, dependencies and mappings (i.e. CyVisualPropertyProperties, CyVisualPropertyDependencies and CyVisualPropertyMappings objects) are unique in name. By default, the duplicate attributes are updated with the values of the latest one. This can prevented by setting the replace parameter to FALSE, in that case only new attributes are added and the existing attributes remain untouched. Furthermore, if duplicated attributes are considered as a preventable mistake, an error can be raised by setting stopOnDuplicates to TRUE. This forces the function to stop and raise an error, if duplicated attributes are present.

Value

CyVisualProperty, CyVisualPropertyProperties, CyVisualPropertyDependencies or CyVisualPropertyMappings objects

See Also

getCyVisualProperty, updateCyVisualProperties

Examples

## Prepare used properties
## Visual property: Properties
vpPropertyP1 = createCyVisualPropertyProperties(c(NODE_BORDER_STROKE="SOLID"))
vpPropertyP2 = createCyVisualPropertyProperties(c(NODE_BORDER_WIDTH="1.5"))
vpPropertyP3 = createCyVisualPropertyProperties(c(NODE_BORDER_WIDTH="999"))

## Add two properties:
vpPropertyP4 = updateCyVisualProperty(vpPropertyP1,vpPropertyP2)
vpPropertyP4 = updateCyVisualProperty(vpPropertyP4,vpPropertyP3)

## Visual property: Dependencies
vpPropertyD1 = createCyVisualPropertyDependencies(c(nodeSizeLocked="false"))
vpPropertyD2 = createCyVisualPropertyDependencies(c(arrowColorMatchesEdge="true"))
vpPropertyD3 = createCyVisualPropertyDependencies(c(arrowColorMatchesEdge="false"))

## Add two dependencies:
vpPropertyD4 = updateCyVisualProperty(vpPropertyD1,vpPropertyD2)
vpPropertyD4 = updateCyVisualProperty(vpPropertyD4,vpPropertyD3)

## Visual property: Mappings
vpPropertyM1 = createCyVisualPropertyMappings(c(NODE_FILL_COLOR="CONTINUOUS"), 
                                              "COL=directed,T=boolean,K=0=true,V=0=ARROW")
vpPropertyM2 = createCyVisualPropertyMappings(c(EDGE_TARGET_ARROW_SHAPE="DISCRETE"), 
                                              "TRIANGLE")
vpPropertyM3 = createCyVisualPropertyMappings(c(EDGE_TARGET_ARROW_SHAPE="DISCRETE"), 
                                              "NONE")

## Add two mappings:
vpPropertyM4 = updateCyVisualProperty(vpPropertyM1,vpPropertyM2)
vpPropertyM4 = updateCyVisualProperty(vpPropertyM4,vpPropertyM3)

## Create visual property object 
vpProperty1 = 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,
                                              NA))
vpProperty2 = createCyVisualProperty(properties=vpPropertyP2, 
                                     dependencies=vpPropertyD2, 
                                     mappings=vpPropertyM2)
vpProperty3 = createCyVisualProperty(properties=vpPropertyP3, 
                                     dependencies=vpPropertyD3, 
                                     mappings=vpPropertyM3)

## add two visual property objects
vpProperty4 = updateCyVisualProperty(vpProperty1, vpProperty2)

## update values
updateCyVisualProperty(vpProperty4, vpProperty3)

## keep old values
updateCyVisualProperty(vpProperty4, vpProperty3, 
                       replace = FALSE)

## keep old values
try(updateCyVisualProperty(vpProperty4, vpProperty3, 
                           stopOnDuplicates = TRUE))
## =>ERROR: 
## Elements of name (in properties<appliesTo=NA,view=NA>) must not contain duplicates!

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