# Functions to Access and Control Cytoscape

## Documentation for package ‘RCy3’ version 2.0.88

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

## Help Pages

A C D E F G H I L M N O P R S T U

RCy3-package | RCy3: Functions to Access and Control Cytoscape

## -- A --

addCyEdge | DEFUNCT: addCyEdge
addCyEdgedefunct | DEFUNCT: addCyEdge
addCyEdges | Add CyEdges
addCyNode | DEFUNCT: addCyNode
addCyNodedefunct | DEFUNCT: addCyNode
addCyNodes | Add CyNodes
addGraphToGraph | DEFUNCT: addGraphToGraph
addGraphToGraphdefunct | DEFUNCT: addGraphToGraph
AddToGroup | Add to Group

## -- C --

clearEdgePropertyBypass | Clear Edge Property Bypass
clearNetworkCenterBypass | Clear Network Center Bypass
clearNetworkPropertyBypass | Clear Network Property Bypass
clearNetworkZoomBypass | Clear Network Zoom Bypass
clearNodeOpacityBypass | Clear Node Opacity Bypass
clearNodePropertyBypass | Clear Node Property Bypass
clearSelection | Clear Selection
cloneNetwork | Clone a Cytoscape Network
closeSession | Close Session
collapseGroup | Collapse Group
commandEcho | Command Echo
commandOpenDialog | Command Open Dialog
commandPause | Command Pause
commandQuit | Command Quit
commandRunFile | Command Run File
commandsAPI | Open Swagger docs for CyREST Commands API
commandsGET | Commands GET
commandsHelp | Commands Help
commandSleep | Command Sleep
commandsPOST | Commands POST
commandsRun | Run a Command
connectToNewestCyWindow | DEFUNCT: connectToNewestCyWindow
connectToNewestCyWindowdefunct | DEFUNCT: connectToNewestCyWindow
copyCytoscapeNetwork | DEPRECATED: copyCytoscapeNetwork
copyCytoscapeNetworkdeprecated | DEPRECATED: copyCytoscapeNetwork
copyVisualStyle | Copy Visual Style
createGraphFromNetwork | createGraphFromNetwork
createGroup | Create Group
createIgraphFromNetwork | Create an igraph network from a Cytoscape network
createNetworkFromDataFrames | Create a network from data frames
createNetworkFromGraph | Create Network From Graph
createNetworkFromIgraph | Create a Cytoscape network from an igraph network
createSubnetwork | Create subnetwork from existing network
createVisualStyle | Create a visual style from components
createWindow | DEPRECATED: createWindow
createWindowdeprecated | DEPRECATED: createWindow
createWindowFromSelection | DEPRECATED: createWindowFromSelection
createWindowFromSelectiondeprecated | DEPRECATED: createWindowFromSelection
cy2.edge.names | DEFUNCT: cy2.edge.names
cy2.edge.namesdefunct | DEFUNCT: cy2.edge.names
cybrowserClose | Cybrowser Close
cybrowserDialog | Cybrowser Dialog
cybrowserHide | Cybrowser Hide
cybrowserList | Cybrowser List
cybrowserSend | Cybrowser Send
cybrowserShow | Cybrowser Show
cybrowserVersion | Cybrowser Version
cyPlot | DEFUNCT: cyPlot
cyPlotdefunct | DEFUNCT: cyPlot
cyrestAPI | Open Swagger docs for CyREST API
cyrestDELETE | CyREST DELETE
cyrestGET | CyREST GET
cyrestPOST | CyREST POST
cyrestPUT | CyREST PUT
cytoscapeApiVersions | Available CyREST API Versions
CytoscapeConnection | DEPRECATED: CytoscapeConnection
CytoscapeConnectiondeprecated | DEPRECATED: CytoscapeConnection
cytoscapeFreeMemory | Free Up Unused Memory for Cytoscape
cytoscapeMemoryStatus | Memory Available to Cytoscape
cytoscapeNumberOfCores | Number of Processors Available to Cytoscape
cytoscapePing | Ping Cytoscape
cytoscapeVersionInfo | Cytoscape and CyREST API Versions
CytoscapeWindow | DEPRECATED: CytoscapeWindow
CytoscapeWindowdeprecated | DEPRECATED: CytoscapeWindow

## -- D --

deleteAllNetworks | Delete All Networks
deleteAllWindows | DEPRECATED: deleteAllWindows
deleteAllWindowsdeprecated | DEPRECATED: deleteAllWindows
deleteEdgeAttribute | DEPRECATED: deleteEdgeAttribute
deleteEdgeAttribute_deprecated | DEPRECATED: deleteEdgeAttribute
deleteGroup | Delete (or Ungroup) a Group
deleteNetwork | Delete Network
deleteNodeAttribute | DEPRECATED: deleteNodeAttribute
deleteNodeAttribute_deprecated | DEPRECATED: deleteNodeAttribute
deleteSelectedEdges | Delete Selected Edges
deleteSelectedNodes | Delete Selected Nodes
deleteTableColumn | Delete a table column
deleteWindow | DEPRECATED: deleteWindow
deleteWindowdeprecated | DEPRECATED: deleteWindow
demoSimpleGraph | DEFUNCT: demoSimpleGraph
demoSimpleGraphdefunct | DEFUNCT: demoSimpleGraph
diffusionAdvanced | Diffusion Advanced
diffusionBasic | Diffusion Basic
disableApp | Disable App
displayGraph | DEFUNCT: displayGraph
displayGraphdefunct | DEFUNCT: displayGraph
dockPanel | Dock Panel

## -- E --

eda | DEFUNCT: eda
eda.names | DEFUNCT: eda.names
eda.namesdefunct | DEFUNCT: eda.names
edadefunct | DEFUNCT: eda
enableApp | Enable App
existing.CytoscapeWindow | DEPRECATED: existing.CytoscapeWindow
existing.CytoscapeWindowdeprecated | DEPRECATED: existing.CytoscapeWindow
expandGroup | Expand Group
exportImage | Export Image
exportNetwork | Export Network
exportNetworkToNDEx | Export Network To NDEx
exportVisualStyles | Export Visual Styles

## -- F --

fitContent | Fit Content
fitSelectedContent | DEPRECATED: fitSelectedContent
fitSelectedContent_deprecated | DEPRECATED: fitSelectedContent
floatPanel | Float Panel

## -- G --

getAdjacentEdgeNames | DEFUNCT: getAdjacentEdgeNames
getAdjacentEdgeNamesdefunct | DEFUNCT: getAdjacentEdgeNames
getAllEdgeAttributes | DEPRECATED: getAllEdgeAttributes
getAllEdgeAttributes_deprecated | DEPRECATED: getAllEdgeAttributes
getAllEdges | Get All Edges
getAllNodeAttributes | DEPRECATED: getAllNodeAttributes
getAllNodeAttributes_deprecated | DEPRECATED: getAllNodeAttributes
getAllNodes | Get All Nodes
getAppInformation | Get App Information
getAppStatus | App Status
getAppUpdates | List Apps With Updates
getArrowShapes | Get Arrow Shapes
getAttributeClassNames | DEFUNCT: getAttributeClassNames
getAttributeClassNamesdefunct | DEFUNCT: getAttributeClassNames
getAvailableApps | List Available Apps
getBackgroundColorDefault | Get Background Color Default
getCenter | DEPRECATED: getCenter
getCenterdeprecated | DEPRECATED: getCenter
getCollectionList | Get Collection List
getCollectionName | Get Collection Name
getCollectionNetworks | Get Collection Networks
getCollectionSuid | Get Collection Suid
getCommandNames | DEPRECATED: getCommandNames
getCommandNamesWithinNamespace | DEPRECATED: getCommandNamesWithinNamespace
getCommandNamesWithinNamespace_deprecated | DEPRECATED: getCommandNamesWithinNamespace
getCommandNames_deprecated | DEPRECATED: getCommandNames
getDefaultEdgeReverseSelectionColor | DEFUNCT: getDefaultEdgeReverseSelectionColor
getDefaultEdgeReverseSelectionColordefunct | DEFUNCT: getDefaultEdgeReverseSelectionColor
getDefaultNodeReverseSelectionColor | DEFUNCT: getDefaultNodeReverseSelectionColor
getDefaultNodeReverseSelectionColordefunct | DEFUNCT: getDefaultNodeReverseSelectionColor
getDirectlyModifiableVisualProperties | DEPRECATED: getDirectlyModifiableVisualProperties
getDirectlyModifiableVisualPropertiesdeprecated | DEPRECATED: getDirectlyModifiableVisualProperties
getDisabledApps | List Disabled Apps
getEdgeAttribute | DEPRECATED: getEdgeAttribute
getEdgeAttributeNames | DEPRECATED: getEdgeAttributeNames
getEdgeAttributeNames_deprecated | DEPRECATED: getEdgeAttributeNames
getEdgeAttribute_deprecated | DEPRECATED: getEdgeAttribute
getEdgeColor | Get Edge Color
getEdgeCount | Get Edge Count
getEdgeLineStyle | Get Edge Line Style
getEdgeLineWidth | Get Edge Line Width
getEdgeProperty | Get Edge Property Values
getEdgeSelectionColorDefault | Get Edge Selection Color Default
getEdgeTargetArrowShape | Get Edge Target Arrow Shape
getFirstNeighbors | Get list of nodes neighboring provided list
getGraph | DEFUNCT: getGraph
getGraphdefunct | DEFUNCT: getGraph
getGraphFromCyWindow | DEPRECATED: getGraphFromCyWindow
getGraphFromCyWindowdeprecated | DEPRECATED: getGraphFromCyWindow
getGroupInfo | Get Group Information
getInstalledApps | List Installed Apps
getLayoutNameMapping | Get Layout Name Mapping
getLayoutNames | Get Layout Names
getLayoutPropertyNames | Get Layout Property Names
getLayoutPropertyType | Get Layout Property Type
getLayoutPropertyValue | Get Layout Property Value
getLineStyles | Get Line Styles
getNetworkCenter | Get Network Center
getNetworkCount | Get the number of Cytoscape networks
getNetworkList | Get the list of Cytoscape networks
getNetworkName | Get the name of a network
getNetworkNDExId | Get Network NDEx Id
getNetworkProperty | Get Network Property Values
getNetworkSuid | Get the SUID of a network
getNetworkViews | Get Network Views
getNetworkViewSuid | Get the SUID of a network view
getNetworkZoom | Get Network Zoom
getNodeAttribute | DEPRECATED: getNodeAttribute
getNodeAttributeNames | DEPRECATED: getNodeAttributeNames
getNodeAttributeNames_deprecated | DEPRECATED: getNodeAttributeNames
getNodeAttribute_deprecated | DEPRECATED: getNodeAttribute
getNodeColor | Get Node Color
getNodeCount | Get Node Count
getNodeHeight | Get Node Height
getNodePosition | DEFUNCT: getNodePosition
getNodePositiondefunct | DEFUNCT: getNodePosition
getNodeProperty | Get Node Property Values
getNodeSelectionColorDefault | Get Node Selection Color Default
getNodeShapes | Get Node Shapes
getNodeSize | Get Node Size
getNodeWidth | Get Node Width
getSelectedEdgeCount | Get Selected Edge Count
getSelectedEdges | Get Selected Edges
getSelectedNodeCount | Get Selected Node Count
getSelectedNodes | Get Selected Nodes
getStyleDependencies | Get the values of dependencies in a style
getTableColumnNames | Get Table Column Names
getTableColumns | Get table column values
getTableColumnTypes | Get Table Column Types
getTableValue | Get table cell value
getUninstalledApps | List Uninstalled Apps
getViewCoordinates | DEFUNCT: getViewCoordinates
getViewCoordinatesdefunct | DEFUNCT: getViewCoordinates
getVisualPropertyDefault | Get Visual Property Default
getVisualPropertyNames | Get Visual Property Names
getVisualStyleNames | Get Visual Style Names
getWindowCount | DEPRECATED: getWindowCount
getWindowCountdeprecated | DEPRECATED: getWindowCount
getWindowID | DEPRECATED: getWindowID
getWindowIDdeprecated | DEPRECATED: getWindowID
getWindowList | DEPRECATED: getWindowList
getWindowListdeprecated | DEPRECATED: getWindowList
getZoom | DEPRECATED: getZoom
getZoomdeprecated | DEPRECATED: getZoom

## -- H --

hideAllPanels | Hide All Panels
hideEdges | Hide Edges
hideNodes | Hide Nodes
hidePanel | Hide Panel
hideSelectedEdges | Hide Selected Edges
hideSelectedNodes | Hide Selected Nodes

## -- I --

importNetworkFromFile | Import Network From File
importNetworkFromNDEx | Import Network From NDEx
initEdgeAttribute | DEFUNCT: initEdgeAttribute
initEdgeAttributedefunct | DEFUNCT: initEdgeAttribute
initNodeAttribute | DEFUNCT: initNodeAttribute
initNodeAttributedefunct | DEFUNCT: initNodeAttribute
installApp | Install App
invertEdgeSelection | Invert Edge Selection
invertNodeSelection | Invert Node Selection

## -- L --

layoutCopycat | Copy a layout from one network to another
layoutNetwork | Apply a layout to a network
listGroups | List Groups
loadTableData | Loads data into Cytoscape tables keyed by row
lockNodeDimensions | Lock Node Dimensions

## -- M --

makeRandomGraph | DEFUNCT: makeRandomGraph
makeRandomGraphdefunct | DEFUNCT: makeRandomGraph
makeSimpleGraph | Make Simple Graph
makeSimpleIgraph | Make Simple Igraph
mapTableColumn | Map Table Column
mapVisualProperty | Creates a mapping between an attribute and a visual property
matchArrowColorToEdge | Match Arrow Color To Edge

## -- N --

noa | DEFUNCT: noa
noa.names | DEFUNCT: noa.names
noa.namesdefunct | DEFUNCT: noa.names
noadefunct | DEFUNCT: noa

## -- O --

openAppStore | Open App Store Page
openSession | Open Session File or URL

## -- P --

ping | DEPRECATED: ping
ping_deprecated | DEPRECATED: ping
pluginVersion | DEPRECATED: pluginVersion
pluginVersiondeprecated | DEPRECATED: pluginVersion
predictTimeToDisplayGraph | DEFUNCT: predictTimeToDisplayGraph
predictTimeToDisplayGraphdefunct | DEFUNCT: predictTimeToDisplayGraph

## -- R --

raiseWindow | DEFUNCT: raiseWindow
raiseWindowdefunct | DEFUNCT: raiseWindow
RCy3 | RCy3: Functions to Access and Control Cytoscape
redraw | DEPRECATED: redraw
redrawdeprecated | DEPRECATED: redraw
RemoveFromGroup | Remove from Group
renameCytoscapeNetwork | DEPRECATED: renameCytoscapeNetwork
renameCytoscapeNetworkdeprecated | DEPRECATED: renameCytoscapeNetwork
renameNetwork | Rename a network
renameTableColumn | Rename Table Column
restoreLayout | DEFUNCT: restoreLayout
restoreLayoutdefunct | DEFUNCT: restoreLayout

## -- S --

saveImage | DEPRECATED: saveImage
saveImagedeprecated | DEPRECATED: saveImage
saveLayout | DEFUNCT: saveLayout
saveLayoutdefunct | DEFUNCT: saveLayout
saveNetwork | DEPRECATED: saveNetwork
saveNetwork_deprecated | DEPRECATED: saveNetwork
saveSession | Save Session to File
selectAllEdges | Select all edges
selectAllNodes | Select all nodes
selectEdges | Select Edges
selectEdgesAdjacentToSelectedNodes | Select Edges Adjacent To Selected Nodes
selectEdgesConnectedBySelectedNodes | DEPRECATED: selectEdgesConnectedBySelectedNodes
selectEdgesConnectedBySelectedNodes_deprecated | DEPRECATED: selectEdgesConnectedBySelectedNodes
selectEdgesConnectingSelectedNodes | Select the edges connecting selected nodes in Cytoscape Network
selectFirstNeighbors | Select first neighbor nodes
selectFirstNeighborsOfSelectedNodes | DEPRECATED: selectFirstNeighborsOfSelectedNodes
selectFirstNeighborsOfSelectedNodesdeprecated | DEPRECATED: selectFirstNeighborsOfSelectedNodes
selectNodes | Select Nodes
sendEdges | DEFUNCT: sendEdges
sendEdgesdefunct | DEFUNCT: sendEdges
sendNodes | DEFUNCT: sendNodes
sendNodesdefunct | DEFUNCT: sendNodes
setBackgroundColorDefault | Set Background Color Default
setCenter | DEPRECATED: setCenter
setCenterdeprecated | DEPRECATED: setCenter
setCommandProperties | DEFUNCT: setCommandProperties
setCommandPropertiesdefunct | DEFUNCT: setCommandProperties
setCurrentNetwork | Set current network
setCurrentView | Set Current View
setDefaultEdgeReverseSelectionColor | DEFUNCT: setDefaultEdgeReverseSelectionColor
setDefaultEdgeReverseSelectionColordefunct | DEFUNCT: setDefaultEdgeReverseSelectionColor
setDefaultNodeReverseSelectionColor | DEFUNCT: setDefaultNodeReverseSelectionColor
setDefaultNodeReverseSelectionColordefunct | DEFUNCT: setDefaultNodeReverseSelectionColor
setEdgeAttributes | DEFUNCT: setEdgeAttributes
setEdgeAttributesdefunct | DEFUNCT: setEdgeAttributes
setEdgeColorBypass | Set Edge Color Bypass
setEdgeColorDefault | Set Edge Color Default
setEdgeColorMapping | Set Edge Color Mapping
setEdgeFontFaceBypass | Set Edge Font Face Bypass
setEdgeFontSizeBypass | Set Edge Font Size Bypass
setEdgeFontSizeDefault | Set Edge Font Size Default
setEdgeLabelBypass | Set Edge Label Bypass
setEdgeLabelColorBypass | Set Edge Label Color Bypass
setEdgeLabelMapping | Set Edge Label Mapping
setEdgeLabelOpacityBypass | Set Edge Label Opacity Bypass
setEdgeLineStyleBypass | Set Edge Line Style Bypass
setEdgeLineStyleDefault | Set Edge Line Style Default
setEdgeLineStyleMapping | Set Edge Line Style Mapping
setEdgeLineWidthBypass | Set Edge Line Width Bypass
setEdgeLineWidthDefault | Set Edge Line Width Default
setEdgeLineWidthMapping | Set Edge Line Width Mapping
setEdgeOpacityBypass | Set Edge Opacity Bypass
setEdgeOpacityMapping | Set Edge Opacity Mapping
setEdgePropertyBypass | Set Edge Property Bypass
setEdgeSelectionColorDefault | Set Edge Selection Color Default
setEdgeSourceArrowColorBypass | Set Edge Source Arrow Color Bypass
setEdgeSourceArrowColorDefault | Set Edge Source Arrow Color Default
setEdgeSourceArrowColorMapping | Set Edge Source Arrow Color Mapping
setEdgeSourceArrowMapping | Set Edge Source Arrow Mapping
setEdgeSourceArrowShapeBypass | Set Edge Source Arrow Shape Bypass
setEdgeSourceArrowShapeDefault | Set Edge Source Arrow Shape Default
setEdgeTargetArrowColorBypass | Set Edge Target Arrow Color Bypass
setEdgeTargetArrowColorDefault | Set Edge Target Arrow Color Default
setEdgeTargetArrowColorMapping | Set Edge Target Arrow Color Mapping
setEdgeTargetArrowMapping | Set Edge Target Arrow Mapping
setEdgeTargetArrowShapeBypass | Set Edge Target Arrow Shape Bypass
setEdgeTargetArrowShapeDefault | Set Edge Target Arrow Shape Default
setEdgeTooltipBypass | Set Edge Tooltip Bypass
setEdgeTooltipMapping | Set Edge Tooltip Mapping
setGraph | DEFUNCT: setGraph
setGraphdefunct | DEFUNCT: setGraph
setLayoutProperties | Set Layout Properties
setNetworkCenterBypass | Set Network Center Bypass
setNetworkPropertyBypass | Set Network Property Bypass
setNetworkZoomBypass | Set Network Zoom Bypass
setNodeAttributes | DEFUNCT: setNodeAttributes
setNodeAttributesdefunct | DEFUNCT: setNodeAttributes
setNodeBorderColorBypass | Set Node Border Color Bypass
setNodeBorderColorDefault | Set Node Border Color Default
setNodeBorderColorMapping | Set Node Border Color Mapping
setNodeBorderOpacityBypass | Set Node Border Opacity Bypass
setNodeBorderWidthBypass | Set Node Border Width Bypass
setNodeBorderWidthDefault | Set Node Border Width Default
setNodeBorderWidthMapping | Set Node Border Width Mapping
setNodeColorBypass | Set Node Color Bypass
setNodeColorDefault | Set Node Color Default
setNodeColorMapping | Set Node Color Mapping
setNodeComboOpacityMapping | Set Node Combo Opacity Mapping
setNodeFillOpacityBypass | Set Node Fill Opacity Bypass
setNodeFontSizeBypass | Set Node Font Size Bypass
setNodeFontSizeDefault | Set Node Font Size Default
setNodeHeightBypass | Set Node Height Bypass
setNodeLabelBypass | Set Node Label Bypass
setNodeLabelColorBypass | Set Node Label Color Bypass
setNodeLabelColorDefault | Set Node Label Color Default
setNodeLabelMapping | Set Node Label Mapping
setNodeLabelOpacityBypass | Set Node Label Opacity Bypass
setNodeOpacityBypass | Set Node Opacity Bypass
setNodePosition | DEFUNCT: setNodePosition
setNodePositiondefunct | DEFUNCT: setNodePosition
setNodePropertyBypass | Set Node Property Bypass
setNodeSelectionColorDefault | Set Node Selection Color Default
setNodeShapeBypass | Set Node Shape Bypass
setNodeShapeDefault | Set Node Shape Default
setNodeShapeMapping | Set Node Shape Mapping
setNodeSizeBypass | Set Node Size Bypass
setNodeSizeDefault | Set Node Size Default
setNodeSizeMapping | Set Node Size Mapping
setNodeTooltipMapping | Set Node Tooltip Mapping
setNodeWidthBypass | Set Node Width Bypass
setStyleDependencies | Set Style Dependencies
setTooltipDismissDelay | DEFUNCT: setTooltipDismissDelay
setTooltipDismissDelaydefunct | DEFUNCT: setTooltipDismissDelay
setTooltipInitialDelay | DEFUNCT: setTooltipInitialDelay
setTooltipInitialDelaydefunct | DEFUNCT: setTooltipInitialDelay
setVisualPropertyDefault | Set Visual Property Default
setVisualStyle | Set Visual Style
setWindowSize | DEFUNCT: setWindowSize
setWindowSizedefunct | DEFUNCT: setWindowSize
setZoom | DEPRECATED: setZoom
setZoom_deprecated | DEPRECATED: setZoom
sfn | DEPRECATED: sfn
sfndeprecated | DEPRECATED: sfn
showGraphicsDetails | DEPRECATED: showGraphicsDetails
showGraphicsDetails_deprecated | DEPRECATED: showGraphicsDetails
syncNodeCustomGraphicsSize | Sync Node Custom Graphics Size

## -- T --

toggleGraphicsDetails | Toggle Graphics Details

## -- U --

unhideAll | Unhide All
unhideEdges | Unhide Edges
unhideNodes | Unhide Nodes
uninstallApp | Uninstall App
updateApp | Update App
updateNetworkInNDEx | Update Network In NDEx
updateStyleDefaults | Updates the default values of visual properties in a style
updateStyleMapping | Updates a visual property mapping in a style