R package implementing the Cytoscape Exchange (CX) format

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Documentation for package ‘RCX’ version 1.2.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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