Man pages for frankkramer-lab/RCX
R package implementing the Cytoscape Exchange (CX) format
| aspectClasses | aspectClasses and subAspectClasses |
| CartesianLayout | Cartesian layout |
| checks | Checks |
| convert2json | Convert data to json by R class |
| convert-data-types-and-values | Convert data types in 'data.frame(dataType,isList)' to... |
| Convert-Names-and-Classes | Convert aspect class name to RCX accession |
| countElements | Number of elements in aspect |
| 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... |
| CyVisualPropertyDependencies | Create a object for dependency of Cytoscape Visual Properties... |
| CyVisualPropertyMappings | Create an object for mappings of Cytoscape Visual Properties... |
| CyVisualPropertyProperties | Create a object for properties of Cytoscape Visual Properties... |
| dot-addAspectNameToJson | Add the aspect name to the JSON |
| dot-addAttributeData | Add attribute data to an igraph object |
| dot-aspectClass | Get the class of aspects |
| dot-convertRawList | Convert a list of vectors to a character vector with pasted... |
| dot-createAttributeAspect | Create a default *AttributeAspect |
| dot-createCyVpPorD | Helper to create structure for classes... |
| dot-errorCodes | Error codes used in this package |
| dot-filterBy | Filter several parameters for elements, that match to a given... |
| dot-format | Format objects for error logging |
| dot-infer | Infer the data type from values and check if the value... |
| dot-json2RDataType | Get the data type and isList from JSON data |
| dot-jsonL | Return data as a list from a JSON list |
| dot-jsonV | Return data as a vector from a JSON list |
| dot-log | Logging (printing) the results of test cases |
| dot-mergeAttributesAspect | Merge two *AttributeAspects |
| dot-mergeIdAspect | Merge two aspects (data.frames) |
| dot-modClass | Add or remove a class name from an object |
| dot-pasteC | Concatenate as comma separated character vector |
| dot-renameDF | Rename data.frame columns by key-value pairs in rnames |
| dot-stop | Customized stop() function |
| dot-summaryAspect | Helper function to mark columns that are ids or reference ids |
| dot_test | Helping tests |
| dot-transformListLength-set | Transform an aspect with a list as column |
| dot-transformVLD | Transform an aspect with data type |
| dot-validateAttributesAspect | Helper for validating node- and edge-attributes aspects |
| dot-validateCyVisualPropertyPandD | Cytoscape visual property: List of property and dependency |
| EdgeAttributes | Edge attributes |
| Edges | Edges |
| getCyVisualProperty | Get a Cytoscape visual property (object used in... |
| graphNEL | Convert an RCX object from and to an graphNEL object |
| hasIds | IDs of an aspect |
| idProperty | Name of the property of an aspect that is an ID |
| Igraph | Convert an RCX object from and to an igraph object |
| jsonToRCX | Convert parsed JSON aspects to RCX |
| markAttributeColumn | Mark attribute name columns within a data.frame |
| markRefColumn | Mark required and optional references within a data.frame |
| maxId | Highest ID of an aspect |
| Meta-data | Update RCX meta-data |
| NetworkAttributes | Network attributes |
| NodeAttributes | Node attributes |
| Nodes | Nodes |
| RCX | R package implementing the Cytoscape Exchange (CX) format |
| RCX-object | Create an RCX object from aspects |
| rcxToJson | Convert RCX aspects to JSON |
| readCX | Read CX from file, parse the JSON and convert it to an RCX... |
| referredBy | List the aspects that are refered by an other aspect |
| refersTo | Name of the property of an aspect that is an ID |
| setExtension | Set or register an RCX extension |
| summary | RCX and aspect summary |
| toCX | Convert an RCX object to CX (JSON) |
| updateCartesianLayout | Update Cartesian Layouts |
| updateCyGroups | Update Cytoscape Groups |
| updateCyHiddenAttributes | Update Cytoscape hidden attributes |
| updateCyNetworkRelations | Update Cytoscape network relations |
| updateCySubNetworks | Update Cytoscape subnetworks |
| updateCyTableColumn | Update Cytoscape table column properties |
| updateCyVisualProperties | Update Cytoscape Visual Properties (aspect) |
| updateCyVisualProperty | Update Cytoscape Visual Property objects and sub-objects... |
| updateEdgeAttributes | Update edge attributes |
| updateEdges | Update edges |
| updateMetaDataProperties | Update meta-data properties |
| updateNetworkAttributes | Update network attributes |
| updateNodeAttributes | Update node attributes |
| updateNodes | Update nodes |
| validate | Validate RCX and its aspects |
| visualize | Visualize a Network |
| writeCX | Write RCX to file |
| writeHTML | Save network visualization as HTML file |
