A custom aspect | Create the custom aspect in R | Update the aspect | Providing update methods | Update meta-data for the aspect | Witout a extension package | As extension package | Meta-data summary | Aspect references | Convenience methods | Validation of the aspect | Conversion to and from CX | Convert to CX | Conversion from CX/JSON | Session info
Package: RCX 1.17.0
Florian Auer
RCX: R package implementing the Cytoscape Exchange (CX) format
Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.
Authors:
RCX_1.17.0.tar.gz
RCX_1.17.0.zip(r-4.7)RCX_1.17.0.zip(r-4.6)RCX_1.17.0.zip(r-4.5)
RCX_1.17.0.tgz(r-4.6-any)RCX_1.17.0.tgz(r-4.5-any)
RCX_1.17.0.tar.gz(r-4.7-any)RCX_1.17.0.tar.gz(r-4.6-any)
RCX_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RCX/json (API)
| # Install 'RCX' in R: |
| install.packages('RCX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/frankkramer-lab/rcx/issues
On BioConductor:RCX-1.17.0(bioc 3.24)RCX-1.16.0(bioc 3.23)
Last updated from:ae8457eaef. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 169 | ||
| linux-devel-x86_64 | OK | 269 | ||
| source / vignettes | OK | 241 | ||
| linux-release-x86_64 | OK | 219 | ||
| macos-release-arm64 | OK | 121 | ||
| macos-oldrel-arm64 | OK | 93 | ||
| windows-devel | OK | 102 | ||
| windows-release | OK | 95 | ||
| windows-oldrel | OK | 93 | ||
| wasm-release | OK | 148 |
Exports:.markAttributeColumn<-.markRefColumn<-aspectClass2NameaspectClassesaspectName2ClasscountElementscreateCartesianLayoutcreateCyGroupscreateCyHiddenAttributescreateCyNetworkRelationscreateCySubNetworkscreateCyTableColumncreateCyVisualPropertiescreateCyVisualPropertycreateCyVisualPropertyDependenciescreateCyVisualPropertyMappingscreateCyVisualPropertyPropertiescreateEdgeAttributescreateEdgescreateNetworkAttributescreateNodeAttributescreateNodescreateRCXfromGraphNELfromIgraphgetAspectClassesgetCyVisualPropertyhasIdsidPropertyjsonToRCXmaxIdparseJSONprocessCXrcxToJsonreadCXreadJSONreferredByrefersTosetExtensionsubAspectClassestoCXtoGraphNELtoIgraphupdateAspectClassesupdateCartesianLayoutupdateCyGroupsupdateCyHiddenAttributesupdateCyNetworkRelationsupdateCySubNetworksupdateCyTableColumnupdateCyVisualPropertiesupdateCyVisualPropertyupdateEdgeAttributesupdateEdgesupdateMetaDataupdateMetaDataPropertiesupdateNetworkAttributesupdateNodeAttributesupdateNodesvalidatevisualizewriteCXwriteHTML
Dependencies:clicpp11glueigraphjsonlitelatticelifecyclemagrittrMatrixpkgconfigplyrRcpprlangvctrs
Extending the RCX Data Model
Last update: 2022-12-23
Started: 2021-10-25
RCX - an R package implementing the Cytoscape Exchange (CX) format
Introduction | The Cytoscape Exchange (CX) | The NDEx platform | Cytoscape | RCX - an adaption of the CX format | Installation | The basics | Read and write CX files | Explore the RCX object | Visualize the network | Validation | Get information about the networks | Conversion to R graph data models | igraph | Bioconductor graph (graphNEL) | Session info
Last update: 2022-10-06
Started: 2021-10-25
Creating RCX from scratch
The Cytoscape Exchange (CX) Format | Starting with nodes and edges | Adding attributes to the network | Node Attributes | Network Attributes | Put the nodes into position | Create visual layout | Visual properties of the network | Visual properties of nodes | Visual properties of edges | Create a visual property aspect | Table column | Visualize the final network | Meta-data | Create RCX at once | Save the network | Session info
Last update: 2021-10-25
Started: 2021-10-25
Appendix: The RCX and CX Data Model
CX data structure | Aspect dependencies | Data types | NDEx conventions | Handling of Identifiers | Citations | Meta aspects | metaData | status | Core aspects | nodes | edges | nodeAttributes | edgeAttributes | networkAttributes | cartesianLayout | Cytoscape aspects | cyGroups | CyVisualProperties | CyVisualProperties (CX) | CyVisualProperties (RCX) | CyVisualProperty | CyVisualPropertyProperties | CyVisualPropertyDependencies | CyVisualPropertyMappings | cyHiddenAttributes | cyNetworkRelations | cySubNetworks | cyTableColum | Deprecated aspects | Session info
Last update: 2021-10-25
Started: 2021-10-25
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| aspectClasses and subAspectClasses | aspectClasses getAspectClasses subAspectClasses updateAspectClasses |
| Cartesian layout | CartesianLayout createCartesianLayout |
| Convert aspect class name to RCX accession | aspectClass2Name aspectName2Class Convert-Names-and-Classes |
| Number of elements in aspect | countElements countElements.CyVisualPropertiesAspect countElements.default countElements.MetaDataAspect countElements.RCX |
| Print functions for RCX and aspect classes | custom-print print.CartesianLayoutAspect print.CyGroupsAspect print.CyHiddenAttributesAspect print.CyNetworkRelationsAspect print.CySubNetworksAspect print.CyTableColumnAspect print.CyVisualPropertiesAspect print.CyVisualProperty print.CyVisualPropertyDependencies print.CyVisualPropertyMappings print.CyVisualPropertyProperties print.EdgeAttributesAspect print.EdgesAspect print.MetaDataAspect print.NetworkAttributesAspect print.NodeAttributesAspect print.NodesAspect print.RCX |
| Cytoscape Groups | createCyGroups CyGroups |
| Cytoscape hidden attributes | createCyHiddenAttributes CyHiddenAttributes |
| Cytoscape network relations | createCyNetworkRelations CyNetworkRelations |
| Cytoscape subnetworks | createCySubNetworks CySubNetworks |
| Cytoscape table column properties | createCyTableColumn CyTableColumn |
| Cytoscape visual properties (aspect) | createCyVisualProperties CyVisualProperties |
| Cytoscape visual property (object used in CyVisualProperties aspect) | createCyVisualProperty CyVisualProperty |
| Create a object for dependency of Cytoscape Visual Properties (object used in CyVisualProperty) | createCyVisualPropertyDependencies CyVisualPropertyDependencies |
| Create an object for mappings of Cytoscape Visual Properties (object used in CyVisualProperty) | createCyVisualPropertyMappings CyVisualPropertyMappings |
| Create a object for properties of Cytoscape Visual Properties (object used in CyVisualProperty) | createCyVisualPropertyProperties CyVisualPropertyProperties |
| Edge attributes | createEdgeAttributes EdgeAttributes |
| Edges | createEdges Edges |
| Get a Cytoscape visual property (object used in CyVisualProperties aspect) by appliesTo and view | getCyVisualProperty |
| Convert an RCX object from and to an graphNEL object | fromGraphNEL graphNEL toGraphNEL |
| IDs of an aspect | hasIds hasIds.CyGroupsAspect hasIds.CySubNetworksAspect hasIds.default hasIds.EdgesAspect hasIds.NodesAspect |
| Name of the property of an aspect that is an ID | idProperty idProperty.CyGroupsAspect idProperty.CySubNetworksAspect idProperty.default idProperty.EdgesAspect idProperty.NodesAspect |
| Convert an RCX object from and to an igraph object | fromIgraph Igraph toIgraph |
| Convert parsed JSON aspects to RCX | jsonToRCX jsonToRCX.cartesianLayout jsonToRCX.cyGroups jsonToRCX.cyHiddenAttributes jsonToRCX.cyNetworkRelations jsonToRCX.cySubNetworks jsonToRCX.cyTableColumn jsonToRCX.cyVisualProperties jsonToRCX.default jsonToRCX.edgeAttributes jsonToRCX.edges jsonToRCX.metaData jsonToRCX.networkAttributes jsonToRCX.nodeAttributes jsonToRCX.nodes jsonToRCX.numberVerification jsonToRCX.status |
| Highest ID of an aspect | maxId maxId.default maxId.RCX |
| Update RCX meta-data | Meta-data updateMetaData updateMetaData.default updateMetaData.RCX |
| Network attributes | createNetworkAttributes NetworkAttributes |
| Node attributes | createNodeAttributes NodeAttributes |
| Nodes | createNodes Nodes |
| Create an RCX object from aspects | createRCX RCX-object |
| Convert RCX aspects to JSON | rcxToJson rcxToJson.CartesianLayoutAspect rcxToJson.CyGroupsAspect rcxToJson.CyHiddenAttributesAspect rcxToJson.CyNetworkRelationsAspect rcxToJson.CySubNetworksAspect rcxToJson.CyTableColumnAspect rcxToJson.CyVisualPropertiesAspect rcxToJson.CyVisualProperty rcxToJson.CyVisualPropertyDependencies rcxToJson.CyVisualPropertyMappings rcxToJson.CyVisualPropertyProperties rcxToJson.default rcxToJson.EdgeAttributesAspect rcxToJson.EdgesAspect rcxToJson.MetaDataAspect rcxToJson.NetworkAttributesAspect rcxToJson.NodeAttributesAspect rcxToJson.NodesAspect |
| Read CX from file, parse the JSON and convert it to an RCX object | parseJSON processCX readCX readJSON |
| List the aspects that are refered by an other aspect | referredBy |
| Name of the property of an aspect that is an ID | refersTo refersTo.CartesianLayoutAspect refersTo.CyGroupsAspect refersTo.CySubNetworksAspect refersTo.CyVisualPropertiesAspect refersTo.default refersTo.EdgeAttributesAspect refersTo.EdgesAspect refersTo.NodeAttributesAspect |
| Set or register an RCX extension | setExtension |
| RCX and aspect summary | summary summary.AspectAttributeColumn summary.AspectIdColumn summary.AspectListLengthColumn summary.AspectRefColumn summary.AspectReqRefColumn summary.AspectValueColumn summary.CartesianLayoutAspect summary.CyGroupsAspect summary.CyHiddenAttributesAspect summary.CyNetworkRelationsAspect summary.CySubNetworksAspect summary.CyTableColumnAspect summary.CyVisualPropertiesAspect summary.CyVisualProperty summary.EdgeAttributesAspect summary.EdgesAspect summary.MetaDataAspect summary.NetworkAttributesAspect summary.NodeAttributesAspect summary.NodesAspect summary.RCX |
| Convert an RCX object to CX (JSON) | toCX |
| Update Cartesian Layouts | updateCartesianLayout updateCartesianLayout.CartesianLayoutAspect updateCartesianLayout.RCX |
| Update Cytoscape Groups | updateCyGroups updateCyGroups.CyGroupsAspect updateCyGroups.RCX |
| Update Cytoscape hidden attributes | updateCyHiddenAttributes updateCyHiddenAttributes.CyHiddenAttributesAspect updateCyHiddenAttributes.RCX |
| Update Cytoscape network relations | updateCyNetworkRelations updateCyNetworkRelations.CyNetworkRelationsAspect updateCyNetworkRelations.RCX |
| Update Cytoscape subnetworks | updateCySubNetworks updateCySubNetworks.CySubNetworksAspect updateCySubNetworks.RCX |
| Update Cytoscape table column properties | updateCyTableColumn updateCyTableColumn.CyTableColumnAspect updateCyTableColumn.RCX |
| Update Cytoscape Visual Properties (aspect) | updateCyVisualProperties updateCyVisualProperties.CyVisualPropertiesAspect updateCyVisualProperties.RCX |
| Update Cytoscape Visual Property objects and sub-objects (used in CyVisualProperties aspect) | updateCyVisualProperty updateCyVisualProperty.CyVisualProperty updateCyVisualProperty.CyVisualPropertyDependencies updateCyVisualProperty.CyVisualPropertyMappings updateCyVisualProperty.CyVisualPropertyProperties |
| Update edge attributes | updateEdgeAttributes updateEdgeAttributes.EdgeAttributesAspect updateEdgeAttributes.RCX |
| Update edges | updateEdges updateEdges.EdgesAspect updateEdges.RCX |
| Update meta-data properties | updateMetaDataProperties |
| Update network attributes | updateNetworkAttributes updateNetworkAttributes.NetworkAttributesAspect updateNetworkAttributes.RCX |
| Update node attributes | updateNodeAttributes updateNodeAttributes.NodeAttributesAspect updateNodeAttributes.RCX |
| Update nodes | updateNodes updateNodes.NodesAspect updateNodes.RCX |
| Validate RCX and its aspects | validate validate.CartesianLayoutAspect validate.CyGroupsAspect validate.CyHiddenAttributesAspect validate.CyNetworkRelationsAspect validate.CySubNetworksAspect validate.CyTableColumnAspect validate.CyVisualPropertiesAspect validate.CyVisualProperty validate.CyVisualPropertyDependencies validate.CyVisualPropertyMappings validate.CyVisualPropertyProperties validate.default validate.EdgeAttributesAspect validate.EdgesAspect validate.NetworkAttributesAspect validate.NodeAttributesAspect validate.NodesAspect validate.RCX |
| Visualize a Network | visualize visualize.CX visualize.RCX |
| Write RCX to file | writeCX writeCX.CX writeCX.RCX |
| Save network visualization as HTML file | writeHTML writeHTML.CX writeHTML.RCX |
