Man pages for frankkramer-lab/RCX
R package implementing the Cytoscape Exchange (CX) format

addAttributeDataAdd attribute data to an igraph object
CartesianLayoutCartesian layout
checksChecks
convert2jsonConvert data to json by R class
convert-data-types-and-valuesConvert data types in 'data.frame(dataType,isList)' to...
Convert-Names-and-ClassesConvert aspect class name to RCX accession
countElementsNumber of elements in aspect
custom-printPrint functions for RCX and aspect classes
CyGroupsCytoscape Groups
CyHiddenAttributesCytoscape hidden attributes
CyNetworkRelationsCytoscape network relations
CySubNetworksCytoscape subnetworks
CyTableColumnCytoscape table column properties
CyVisualPropertiesCytoscape visual properties (aspect)
CyVisualPropertyCytoscape visual property (object used in CyVisualProperties...
CyVisualPropertyDependenciesCreate a object for dependency of Cytoscape Visual Properties...
CyVisualPropertyMappingsCreate an object for mappings of Cytoscape Visual Properties...
CyVisualPropertyPropertiesCreate a object for properties of Cytoscape Visual Properties...
dot-addAspectNameToJsonAdd the aspect name to the JSON
dot-aspectClassGet the class of aspects
dot-convertRawListConvert a list of vectors to a character vector with pasted...
dot-createAttributeAspectCreate a default *AttributeAspect
dot-createCyVpPorDHelper to create structure for classes...
dot-errorCodesError codes used in this package
dot-filterByFilter several parameters for elements, that match to a given...
dot-formatFormat objects for error logging
dot-inferInfer the data type from values and check if the value...
dot-json2RDataTypeGet the data type and isList from JSON data
dot-jsonLReturn data as a list from a JSON list
dot-jsonVReturn data as a vector from a JSON list
dot-logLogging (printing) the results of test cases
dot-mergeAttributesAspectMerge two *AttributeAspects
dot-mergeIdAspectMerge two aspects (data.frames)
dot-modClassAdd or remove a class name from an object
dot-pasteCConcatenate as comma separated character vector
dot-renameDFRename data.frame columns by key-value pairs in rnames
dot-stopCustomized stop() function
dot-summaryAspectHelper function to mark columns that are ids or reference ids
dot_testHelping tests
dot-transformListLength-setTransform an aspect with a list as column
dot-transformVLDTransform an aspect with data type
dot-validateAttributesAspectHelper for validating node- and edge-attributes aspects
dot-validateCyVisualPropertyPandDCytoscape visual property: List of property and dependency
EdgeAttributesEdge attributes
EdgesEdges
getCyVisualPropertyGet a Cytoscape visual property (object used in...
hasIdsIDs of an aspect
idPropertyName of the property of an aspect that is an ID
IgraphConvert an RCX object from and to an igraph object
jsonToRCXConvert parsed JSON aspects to RCX
markRefColumnMark required and optional references within a data.frame
maxIdHighest ID of an aspect
Meta-dataUpdate RCX meta-data
NetworkAttributesNetwork attributes
NodeAttributesNode attributes
NodesNodes
RCX-objectCreate an RCX objects from aspects
RCX-packageRCX and RCXgraph data structure package
rcxToJsonConvert RCX aspects to JSON
readCXRead CX from file, parse the JSON and convert it to an RCX...
referedByList the aspects that are refered by an other aspect
refersToName of the property of an aspect that is an ID
summaryRCX and aspect summary
toCXConvert an RCX object to CX (JSON)
updateCartesianLayoutUpdate Cartesian Layouts
updateCyGroupsUpdate Cytoscape Groups
updateCyHiddenAttributesUpdate Cytoscape hidden attributes
updateCyNetworkRelationsUpdate Cytoscape network relations
updateCySubNetworksUpdate Cytoscape subnetworks
updateCyTableColumnUpdate Cytoscape table column properties
updateCyVisualPropertiesUpdate Cytoscape Visual Properties (aspect)
updateCyVisualPropertyUpdate Cytoscape Visual Property objects and sub-objects...
updateEdgeAttributesUpdate edge attributes
updateEdgesUpdate edges
updateMetaDataPropertiesUpdate meta-data properties
updateNetworkAttributesUpdate network attributes
updateNodeAttributesUpdate node attributes
updateNodesUpdate nodes
validateValidate RCX and its aspects
visualizeVisualize a Network
writeCXWrite RCX to file
writeHTMLSave network visualization as HTML file
frankkramer-lab/RCX documentation built on July 14, 2021, 6:33 p.m.