# R package implementing the Cytoscape Exchange (CX) format

## Documentation for package ‘RCX’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C E F G H I J M N P R S T U V W

## -- A --

aspectClass2Name | Convert aspect class name to RCX accession
aspectClasses | aspectClasses and subAspectClasses
aspectName2Class | Convert aspect class name to RCX accession

## -- C --

CartesianLayout | Cartesian layout
Convert-Names-and-Classes | Convert aspect class name to RCX accession
countElements | Number of elements in aspect
countElements.CyVisualPropertiesAspect | Number of elements in aspect
countElements.default | Number of elements in aspect
countElements.MetaDataAspect | Number of elements in aspect
countElements.RCX | Number of elements in aspect
createCartesianLayout | Cartesian layout
createCyGroups | Cytoscape Groups
createCyHiddenAttributes | Cytoscape hidden attributes
createCyNetworkRelations | Cytoscape network relations
createCySubNetworks | Cytoscape subnetworks
createCyTableColumn | Cytoscape table column properties
createCyVisualProperties | Cytoscape visual properties (aspect)
createCyVisualProperty | Cytoscape visual property (object used in CyVisualProperties aspect)
createCyVisualPropertyDependencies | Create a object for dependency of Cytoscape Visual Properties (object used in CyVisualProperty)
createCyVisualPropertyMappings | Create an object for mappings of Cytoscape Visual Properties (object used in CyVisualProperty)
createCyVisualPropertyProperties | Create a object for properties of Cytoscape Visual Properties (object used in CyVisualProperty)
createEdgeAttributes | Edge attributes
createEdges | Edges
createNetworkAttributes | Network attributes
createNodeAttributes | Node attributes
createNodes | Nodes
createRCX | Create an RCX object from aspects
custom-print | Print functions for RCX and aspect classes
CyGroups | Cytoscape Groups
CyHiddenAttributes | Cytoscape hidden attributes
CyNetworkRelations | Cytoscape network relations
CySubNetworks | Cytoscape subnetworks
CyTableColumn | Cytoscape table column properties
CyVisualProperties | Cytoscape visual properties (aspect)
CyVisualProperty | Cytoscape visual property (object used in CyVisualProperties aspect)
CyVisualPropertyDependencies | Create a object for dependency of Cytoscape Visual Properties (object used in CyVisualProperty)
CyVisualPropertyMappings | Create an object for mappings of Cytoscape Visual Properties (object used in CyVisualProperty)
CyVisualPropertyProperties | Create a object for properties of Cytoscape Visual Properties (object used in CyVisualProperty)

## -- E --

EdgeAttributes | Edge attributes
Edges | Edges

## -- F --

fromGraphNEL | Convert an RCX object from and to an graphNEL object
fromIgraph | Convert an RCX object from and to an igraph object

## -- G --

getAspectClasses | aspectClasses and subAspectClasses
getCyVisualProperty | Get a Cytoscape visual property (object used in CyVisualProperties aspect) by appliesTo and view
graphNEL | Convert an RCX object from and to an graphNEL object

## -- H --

hasIds | IDs of an aspect
hasIds.CyGroupsAspect | IDs of an aspect
hasIds.CySubNetworksAspect | IDs of an aspect
hasIds.default | IDs of an aspect
hasIds.EdgesAspect | IDs of an aspect
hasIds.NodesAspect | IDs of an aspect

## -- I --

idProperty | Name of the property of an aspect that is an ID
idProperty.CyGroupsAspect | Name of the property of an aspect that is an ID
idProperty.CySubNetworksAspect | Name of the property of an aspect that is an ID
idProperty.default | Name of the property of an aspect that is an ID
idProperty.EdgesAspect | Name of the property of an aspect that is an ID
idProperty.NodesAspect | Name of the property of an aspect that is an ID
Igraph | Convert an RCX object from and to an igraph object

## -- J --

jsonToRCX | Convert parsed JSON aspects to RCX
jsonToRCX.cartesianLayout | Convert parsed JSON aspects to RCX
jsonToRCX.cyGroups | Convert parsed JSON aspects to RCX
jsonToRCX.cyHiddenAttributes | Convert parsed JSON aspects to RCX
jsonToRCX.cyNetworkRelations | Convert parsed JSON aspects to RCX
jsonToRCX.cySubNetworks | Convert parsed JSON aspects to RCX
jsonToRCX.cyTableColumn | Convert parsed JSON aspects to RCX
jsonToRCX.cyVisualProperties | Convert parsed JSON aspects to RCX
jsonToRCX.default | Convert parsed JSON aspects to RCX
jsonToRCX.edgeAttributes | Convert parsed JSON aspects to RCX
jsonToRCX.edges | Convert parsed JSON aspects to RCX
jsonToRCX.metaData | Convert parsed JSON aspects to RCX
jsonToRCX.networkAttributes | Convert parsed JSON aspects to RCX
jsonToRCX.nodeAttributes | Convert parsed JSON aspects to RCX
jsonToRCX.nodes | Convert parsed JSON aspects to RCX
jsonToRCX.numberVerification | Convert parsed JSON aspects to RCX
jsonToRCX.status | Convert parsed JSON aspects to RCX

## -- M --

maxId | Highest ID of an aspect
maxId.default | Highest ID of an aspect
maxId.RCX | Highest ID of an aspect
Meta-data | Update RCX meta-data

## -- N --

NetworkAttributes | Network attributes
NodeAttributes | Node attributes
Nodes | Nodes

## -- P --

parseJSON | Read CX from file, parse the JSON and convert it to an RCX object
print.CartesianLayoutAspect | Print functions for RCX and aspect classes
print.CyGroupsAspect | Print functions for RCX and aspect classes
print.CyHiddenAttributesAspect | Print functions for RCX and aspect classes
print.CyNetworkRelationsAspect | Print functions for RCX and aspect classes
print.CySubNetworksAspect | Print functions for RCX and aspect classes
print.CyTableColumnAspect | Print functions for RCX and aspect classes
print.CyVisualPropertiesAspect | Print functions for RCX and aspect classes
print.CyVisualProperty | Print functions for RCX and aspect classes
print.CyVisualPropertyDependencies | Print functions for RCX and aspect classes
print.CyVisualPropertyMappings | Print functions for RCX and aspect classes
print.CyVisualPropertyProperties | Print functions for RCX and aspect classes
print.EdgeAttributesAspect | Print functions for RCX and aspect classes
print.EdgesAspect | Print functions for RCX and aspect classes
print.MetaDataAspect | Print functions for RCX and aspect classes
print.NetworkAttributesAspect | Print functions for RCX and aspect classes
print.NodeAttributesAspect | Print functions for RCX and aspect classes
print.NodesAspect | Print functions for RCX and aspect classes
print.RCX | Print functions for RCX and aspect classes
processCX | Read CX from file, parse the JSON and convert it to an RCX object

## -- R --

RCX | R package implementing the Cytoscape Exchange (CX) format
RCX-object | Create an RCX object from aspects
rcxToJson | Convert RCX aspects to JSON
rcxToJson.CartesianLayoutAspect | Convert RCX aspects to JSON
rcxToJson.CyGroupsAspect | Convert RCX aspects to JSON
rcxToJson.CyHiddenAttributesAspect | Convert RCX aspects to JSON
rcxToJson.CyNetworkRelationsAspect | Convert RCX aspects to JSON
rcxToJson.CySubNetworksAspect | Convert RCX aspects to JSON
rcxToJson.CyTableColumnAspect | Convert RCX aspects to JSON
rcxToJson.CyVisualPropertiesAspect | Convert RCX aspects to JSON
rcxToJson.CyVisualProperty | Convert RCX aspects to JSON
rcxToJson.CyVisualPropertyDependencies | Convert RCX aspects to JSON
rcxToJson.CyVisualPropertyMappings | Convert RCX aspects to JSON
rcxToJson.CyVisualPropertyProperties | Convert RCX aspects to JSON
rcxToJson.default | Convert RCX aspects to JSON
rcxToJson.EdgeAttributesAspect | Convert RCX aspects to JSON
rcxToJson.EdgesAspect | Convert RCX aspects to JSON
rcxToJson.MetaDataAspect | Convert RCX aspects to JSON
rcxToJson.NetworkAttributesAspect | Convert RCX aspects to JSON
rcxToJson.NodeAttributesAspect | Convert RCX aspects to JSON
rcxToJson.NodesAspect | Convert RCX aspects to JSON
readCX | Read CX from file, parse the JSON and convert it to an RCX object
readJSON | Read CX from file, parse the JSON and convert it to an RCX object
referredBy | List the aspects that are refered by an other aspect
refersTo | Name of the property of an aspect that is an ID
refersTo.CartesianLayoutAspect | Name of the property of an aspect that is an ID
refersTo.CyGroupsAspect | Name of the property of an aspect that is an ID
refersTo.CySubNetworksAspect | Name of the property of an aspect that is an ID
refersTo.CyVisualPropertiesAspect | Name of the property of an aspect that is an ID
refersTo.default | Name of the property of an aspect that is an ID
refersTo.EdgeAttributesAspect | Name of the property of an aspect that is an ID
refersTo.EdgesAspect | Name of the property of an aspect that is an ID
refersTo.NodeAttributesAspect | Name of the property of an aspect that is an ID

## -- S --

setExtension | Set or register an RCX extension
subAspectClasses | aspectClasses and subAspectClasses
summary | RCX and aspect summary
summary.AspectAttributeColumn | RCX and aspect summary
summary.AspectIdColumn | RCX and aspect summary
summary.AspectListLengthColumn | RCX and aspect summary
summary.AspectRefColumn | RCX and aspect summary
summary.AspectReqRefColumn | RCX and aspect summary
summary.AspectValueColumn | RCX and aspect summary
summary.CartesianLayoutAspect | RCX and aspect summary
summary.CyGroupsAspect | RCX and aspect summary
summary.CyHiddenAttributesAspect | RCX and aspect summary
summary.CyNetworkRelationsAspect | RCX and aspect summary
summary.CySubNetworksAspect | RCX and aspect summary
summary.CyTableColumnAspect | RCX and aspect summary
summary.CyVisualPropertiesAspect | RCX and aspect summary
summary.CyVisualProperty | RCX and aspect summary
summary.EdgeAttributesAspect | RCX and aspect summary
summary.EdgesAspect | RCX and aspect summary
summary.MetaDataAspect | RCX and aspect summary
summary.NetworkAttributesAspect | RCX and aspect summary
summary.NodeAttributesAspect | RCX and aspect summary
summary.NodesAspect | RCX and aspect summary
summary.RCX | RCX and aspect summary

## -- T --

toCX | Convert an RCX object to CX (JSON)
toGraphNEL | Convert an RCX object from and to an graphNEL object
toIgraph | Convert an RCX object from and to an igraph object

## -- U --

updateAspectClasses | aspectClasses and subAspectClasses
updateCartesianLayout | Update Cartesian Layouts
updateCartesianLayout.CartesianLayoutAspect | Update Cartesian Layouts
updateCartesianLayout.RCX | Update Cartesian Layouts
updateCyGroups | Update Cytoscape Groups
updateCyGroups.CyGroupsAspect | Update Cytoscape Groups
updateCyGroups.RCX | Update Cytoscape Groups
updateCyHiddenAttributes | Update Cytoscape hidden attributes
updateCyHiddenAttributes.CyHiddenAttributesAspect | Update Cytoscape hidden attributes
updateCyHiddenAttributes.RCX | Update Cytoscape hidden attributes
updateCyNetworkRelations | Update Cytoscape network relations
updateCyNetworkRelations.CyNetworkRelationsAspect | Update Cytoscape network relations
updateCyNetworkRelations.RCX | Update Cytoscape network relations
updateCySubNetworks | Update Cytoscape subnetworks
updateCySubNetworks.CySubNetworksAspect | Update Cytoscape subnetworks
updateCySubNetworks.RCX | Update Cytoscape subnetworks
updateCyTableColumn | Update Cytoscape table column properties
updateCyTableColumn.CyTableColumnAspect | Update Cytoscape table column properties
updateCyTableColumn.RCX | Update Cytoscape table column properties
updateCyVisualProperties | Update Cytoscape Visual Properties (aspect)
updateCyVisualProperties.CyVisualPropertiesAspect | Update Cytoscape Visual Properties (aspect)
updateCyVisualProperties.RCX | Update Cytoscape Visual Properties (aspect)
updateCyVisualProperty | Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect)
updateCyVisualProperty.CyVisualProperty | Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect)
updateCyVisualProperty.CyVisualPropertyDependencies | Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect)
updateCyVisualProperty.CyVisualPropertyMappings | Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect)
updateCyVisualProperty.CyVisualPropertyProperties | Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect)
updateEdgeAttributes | Update edge attributes
updateEdgeAttributes.EdgeAttributesAspect | Update edge attributes
updateEdgeAttributes.RCX | Update edge attributes
updateEdges | Update edges
updateEdges.EdgesAspect | Update edges
updateEdges.RCX | Update edges
updateMetaData | Update RCX meta-data
updateMetaData.default | Update RCX meta-data
updateMetaData.RCX | Update RCX meta-data
updateMetaDataProperties | Update meta-data properties
updateNetworkAttributes | Update network attributes
updateNetworkAttributes.NetworkAttributesAspect | Update network attributes
updateNetworkAttributes.RCX | Update network attributes
updateNodeAttributes | Update node attributes
updateNodeAttributes.NodeAttributesAspect | Update node attributes
updateNodeAttributes.RCX | Update node attributes
updateNodes | Update nodes
updateNodes.NodesAspect | Update nodes
updateNodes.RCX | Update nodes

## -- V --

validate | Validate RCX and its aspects
validate.CartesianLayoutAspect | Validate RCX and its aspects
validate.CyGroupsAspect | Validate RCX and its aspects
validate.CyHiddenAttributesAspect | Validate RCX and its aspects
validate.CyNetworkRelationsAspect | Validate RCX and its aspects
validate.CySubNetworksAspect | Validate RCX and its aspects
validate.CyTableColumnAspect | Validate RCX and its aspects
validate.CyVisualPropertiesAspect | Validate RCX and its aspects
validate.CyVisualProperty | Validate RCX and its aspects
validate.CyVisualPropertyDependencies | Validate RCX and its aspects
validate.CyVisualPropertyMappings | Validate RCX and its aspects
validate.CyVisualPropertyProperties | Validate RCX and its aspects
validate.default | Validate RCX and its aspects
validate.EdgeAttributesAspect | Validate RCX and its aspects
validate.EdgesAspect | Validate RCX and its aspects
validate.NetworkAttributesAspect | Validate RCX and its aspects
validate.NodeAttributesAspect | Validate RCX and its aspects
validate.NodesAspect | Validate RCX and its aspects
validate.RCX | Validate RCX and its aspects
visualize | Visualize a Network
visualize.CX | Visualize a Network
visualize.RCX | Visualize a Network

## -- W --

writeCX | Write RCX to file
writeCX.CX | Write RCX to file
writeCX.RCX | Write RCX to file
writeHTML | Save network visualization as HTML file
writeHTML.CX | Save network visualization as HTML file
writeHTML.RCX | Save network visualization as HTML file