Functions to Access and Control Cytoscape


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Documentation for package ‘RCy3’ version 2.0.88

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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