Functions to Access and Control Cytoscape


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Documentation for package ‘RCy3’ version 2.14.2

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

-- A --

addAnnotationBoundedText Add Bounded Text Annotation
addAnnotationImage Add Image Annotation
addAnnotationShape Add Shape Annotation
addAnnotationText Add Text Annotation
addCyEdges Add CyEdges
addCyNodes Add CyNodes
AddToGroup Add to Group
analyzeNetwork Analyze Network
applyFilter Apply Filter

-- B --

bundleEdges Bundle Edges

-- C --

checkNotebookIsRunning checkNotebookIsRunning
checkRunningRemote checkRunningRemote
clearEdgeBends Clear Edge Bends
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
copyVisualStyle Copy Visual Style
createColumnFilter Create Column Filter
createCompositeFilter Create Composite Filter
createDegreeFilter Create Degree Filter
createGraphFromNetwork createGraphFromNetwork
createGroup Create Group
createGroupByColumn Create Group by Column
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
cybrowserClose Cybrowser Close
cybrowserDialog Cybrowser Dialog
cybrowserHide Cybrowser Hide
cybrowserList Cybrowser List
cybrowserSend Cybrowser Send
cybrowserShow Cybrowser Show
cybrowserVersion Cybrowser Version
cyrestAPI Open Swagger docs for CyREST API
cyrestDELETE CyREST DELETE
cyrestGET CyREST GET
cyrestPOST CyREST POST
cyrestPUT CyREST PUT
cytoscapeApiVersions Available CyREST API Versions
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

-- D --

deleteAllNetworks Delete All Networks
deleteAnnotation Delete Annotation
deleteDuplicateEdges Delete Duplicate Edges
deleteGroup Delete (or Ungroup) a Group
deleteNetwork Delete Network
deleteSelectedEdges Delete Selected Edges
deleteSelectedNodes Delete Selected Nodes
deleteSelfLoops Delete Self Loops
deleteStyleMapping Delete Style Mapping
deleteTableColumn Delete a table column
deleteVisualStyle Delete Visual Style
diffusionAdvanced Diffusion Advanced
diffusionBasic Diffusion Basic
disableApp Disable App
dockPanel Dock Panel
doInitializeSandbox doInitializeSandbox
doRequestRemote doRequestRemote
doSetSandbox doSetSandbox

-- E --

enableApp Enable App
expandGroup Expand Group
exportFilters Export Filters
exportImage Export Image
exportNetwork Export Network
exportNetworkToNDEx Export Network To NDEx
exportVisualStyles Export Visual Styles

-- F --

findRemoteCytoscape findRemoteCytoscape
fitContent Fit Content
floatPanel Float Panel

-- G --

getAbsSandboxPath getAbsSandboxPath
getAllEdges Get All Edges
getAllNodes Get All Nodes
getAllStyleMappings Get All Style Mappings
getAnnotationList Get Annotation List
getAppInformation Get App Information
getAppStatus App Status
getAppUpdates List Apps With Updates
getArrowShapes Get Arrow Shapes
getAvailableApps List Available Apps
getBackgroundColorDefault Get Background Color Default
getBrowserClientChannel getBrowserClientChannel
getBrowserClientJs getBrowserClientJs
getCollectionList Get Collection List
getCollectionName Get Collection Name
getCollectionNetworks Get Collection Networks
getCollectionSuid Get Collection Suid
getCurrentSandbox getCurrentSandbox
getCurrentSandboxName getCurrentSandboxName
getCurrentSandboxPath getCurrentSandboxPath
getCurrentStyle Get Current Style
getDefaultSandbox getDefaultSandbox
getDefaultSandboxPath getDefaultSandboxPath
getDisabledApps List Disabled Apps
getEdgeColor Get Edge Color
getEdgeCount Get Edge Count
getEdgeInfo Get Edge Information
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
getFilterList Get Filter List
getFirstNeighbors Get list of nodes neighboring provided list
getGroupInfo Get Group Information
getInstalledApps List Installed Apps
getJupyterBridgeURL getJupyterBridgeURL
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
getNodeColor Get Node Color
getNodeCount Get Node Count
getNodeHeight Get Node Height
getNodePosition Get Node Position
getNodeProperty Get Node Property Values
getNodeSelectionColorDefault Get Node Selection Color Default
getNodeShapes Get Node Shapes
getNodeSize Get Node Size
getNodeWidth Get Node Width
getNotebookIsRunning getNotebookIsRunning
getSandboxReinitialize getSandboxReinitialize
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
getStyleMapping Get Style Mapping
getTableColumnNames Get Table Column Names
getTableColumns Get table column values
getTableColumnTypes Get Table Column Types
getTableValue Get table cell value
getUninstalledApps List Uninstalled Apps
getVisualPropertyDefault Get Visual Property Default
getVisualPropertyNames Get Visual Property Names
getVisualStyleNames Get Visual Style Names
groupAnnotation Group Annotation

-- H --

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

-- I --

importFilters Import Filters
importNetworkFromFile Import Network From File
importNetworkFromNDEx Import Network From NDEx
importVisualStyles Import Visual Styles
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 --

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
mergeNetworks Merge Networks

-- N --

notebookExportShowImage notebookExportShowImage
notebookShowImage notebookShowImage

-- O --

openAppStore Open App Store Page
openSession Open Session File or URL

-- P --

paletteColorBrewerAccent paletteColorBrewerAccent Qualitative
paletteColorBrewerBlues paletteColorBrewerBlues Sequential
paletteColorBrewerBrBG paletteColorBrewerBrBG Divergent
paletteColorBrewerBuGn paletteColorBrewerBuGn Sequential
paletteColorBrewerBuPu paletteColorBrewerBuPu Sequential
paletteColorBrewerDark2 paletteColorBrewerDark2 Qualitative
paletteColorBrewerGnBu paletteColorBrewerGnBu Sequential
paletteColorBrewerGreens paletteColorBrewerGreens Sequential
paletteColorBrewerGreys paletteColorBrewerGreys Sequential
paletteColorBrewerOranges paletteColorBrewerOranges Sequential
paletteColorBrewerOrRd paletteColorBrewerOrRd Sequential
paletteColorBrewerPaired paletteColorBrewerPaired Qualitative
paletteColorBrewerPastel1 paletteColorBrewerPastel1 Qualitative
paletteColorBrewerPastel2 paletteColorBrewerPastel2 Qualitative
paletteColorBrewerPiYG paletteColorBrewerPiYG Divergent
paletteColorBrewerPRGn paletteColorBrewerPRGn Divergent
paletteColorBrewerPuBu paletteColorBrewerPuBu Sequential
paletteColorBrewerPuBuGn paletteColorBrewerPuBuGn Sequential
paletteColorBrewerPuOr paletteColorBrewerPuOr Divergent
paletteColorBrewerPuRd paletteColorBrewerPuRd Sequential
paletteColorBrewerPurples paletteColorBrewerPurples Sequential
paletteColorBrewerRdBu paletteColorBrewerRdBu Divergent
paletteColorBrewerRdPu paletteColorBrewerRdPu Sequential
paletteColorBrewerRdYlBu paletteColorBrewerRdYlBu Divergent
paletteColorBrewerReds paletteColorBrewerReds Sequential
paletteColorBrewerSet1 paletteColorBrewerSet1 Qualitative
paletteColorBrewerSet2 paletteColorBrewerSet2 Qualitative
paletteColorBrewerSet3 paletteColorBrewerSet3 Qualitative
paletteColorBrewerYlGn paletteColorBrewerYlGn Sequential
paletteColorBrewerYlGnBu paletteColorBrewerYlGnBu Sequential
paletteColorBrewerYlOrBr paletteColorBrewerYlOrBr Sequential
paletteColorBrewerYlOrRd paletteColorBrewerYlOrRd Sequential
paletteColorRandom paletteColorRandom Qualitative

-- R --

RCy3 RCy3: Functions to Access and Control Cytoscape
RemoveFromGroup Remove from Group
removeNodeCustomGraphics Remove Node Custom Graphics
renameNetwork Rename a network
renameTableColumn Rename Table Column
resetDefaultSandbox resetDefaultSandbox
runningRemoteCheck runningRmoteCheck

-- S --

sandboxGetFileInfo sandboxGetFileInfo
sandboxGetFrom sandboxGetFrom
sandboxInitializer sandboxInitializer
sandboxRemove sandboxRemove
sandboxRemoveFile sandboxRemoveFile
sandboxSendTo sandboxSendTo
sandboxSet sandboxSet
sandboxUrlTo sandboxUrlTo
saveSession Save Session to File
selectAllEdges Select all edges
selectAllNodes Select all nodes
selectEdges Select Edges
selectEdgesAdjacentToSelectedNodes Select Edges Adjacent To Selected Nodes
selectEdgesConnectingSelectedNodes Select the edges connecting selected nodes in Cytoscape Network
selectFirstNeighbors Select first neighbor nodes
selectNodes Select Nodes
selectNodesConnectedBySelectedEdges Select Nodes Connected By Selected Edges
setBackgroundColorDefault Set Background Color Default
setCatchupFilterSecs Set Catchup Filter Delay
setCatchupNetworkSecs Set Catchup Network Delay
setCurrentNetwork Set current network
setCurrentSandbox setCurrentSandbox
setCurrentView Set Current View
setDefaultSandbox setDefaultSandbox
setDefaultSandboxPath setDefaultSandboxPath
setEdgeColorBypass Set Edge Color Bypass
setEdgeColorDefault Set Edge Color Default
setEdgeColorMapping Set Edge Color Mapping
setEdgeFontFaceBypass Set Edge Font Face Bypass
setEdgeFontFaceDefault Set Edge Font Face Default
setEdgeFontFaceMapping Set Edge Font Face Mapping
setEdgeFontSizeBypass Set Edge Font Size Bypass
setEdgeFontSizeDefault Set Edge Font Size Default
setEdgeFontSizeMapping Set Edge Font Size Mapping
setEdgeLabelBypass Set Edge Label Bypass
setEdgeLabelColorBypass Set Edge Label Color Bypass
setEdgeLabelColorDefault Set Edge Label Color Default
setEdgeLabelColorMapping Set Edge Label Color Mapping
setEdgeLabelDefault Set Edge Label Default
setEdgeLabelMapping Set Edge Label Mapping
setEdgeLabelOpacityBypass Set Edge Label Opacity Bypass
setEdgeLabelOpacityDefault Set Edge Label Opacity Default
setEdgeLabelOpacityMapping Set Edge Label Opacity Mapping
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
setEdgeOpacityDefault Set Edge Opacity Default
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
setEdgeSourceArrowShapeMapping Set Edge Source Arrow Shape Mapping
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
setEdgeTargetArrowShapeMapping Set Edge Target Arrow Shape Mapping
setEdgeTooltipBypass Set Edge Tooltip Bypass
setEdgeTooltipDefault Set Edge Tooltip Default
setEdgeTooltipMapping Set Edge Tooltip Mapping
setLayoutProperties Set Layout Properties
setModelPropagationSecs Set Model Propagation Delay
setNetworkCenterBypass Set Network Center Bypass
setNetworkPropertyBypass Set Network Property Bypass
setNetworkZoomBypass Set Network Zoom Bypass
setNodeBorderColorBypass Set Node Border Color Bypass
setNodeBorderColorDefault Set Node Border Color Default
setNodeBorderColorMapping Set Node Border Color Mapping
setNodeBorderOpacityBypass Set Node Border Opacity Bypass
setNodeBorderOpacityDefault Set Node Border Opacity Default
setNodeBorderOpacityMapping Set Node Border Opacity Mapping
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
setNodeCustomBarChart Set Node Custom Bar Chart
setNodeCustomBoxChart Set Node Custom Box Chart
setNodeCustomHeatMapChart Set Node Custom HeatMap Chart
setNodeCustomLinearGradient Set Node Custom Linear Gradient
setNodeCustomLineChart Set Node Custom Line Chart
setNodeCustomPieChart Set Node Custom Pie Chart
setNodeCustomPosition Set Node Custom Position
setNodeCustomRadialGradient Set Node Custom Radial Gradient
setNodeCustomRingChart Set Node Custom Ring Chart
setNodeFillOpacityBypass Set Node Fill Opacity Bypass
setNodeFillOpacityDefault Set Node Fill Opacity Default
setNodeFillOpacityMapping Set Node Fill Opacity Mapping
setNodeFontFaceBypass Set Node Font Face Bypass
setNodeFontFaceDefault Set Node Font Face Default
setNodeFontFaceMapping Set Node Font Face Mapping
setNodeFontSizeBypass Set Node Font Size Bypass
setNodeFontSizeDefault Set Node Font Size Default
setNodeFontSizeMapping Set Node Font Size Mapping
setNodeHeightBypass Set Node Height Bypass
setNodeHeightDefault Set Node Height Default
setNodeHeightMapping Set Node Height Mapping
setNodeLabelBypass Set Node Label Bypass
setNodeLabelColorBypass Set Node Label Color Bypass
setNodeLabelColorDefault Set Node Label Color Default
setNodeLabelColorMapping Set Node Label Color Mapping
setNodeLabelDefault Set Node Label Default
setNodeLabelMapping Set Node Label Mapping
setNodeLabelOpacityBypass Set Node Label Opacity Bypass
setNodeLabelOpacityDefault Set Node Label Opacity Default
setNodeLabelOpacityMapping Set Node Label Opacity Mapping
setNodeOpacityBypass Set Node Opacity Bypass
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
setNodeTooltipBypass Set Node Tooltip Bypass
setNodeTooltipDefault Set Node Tooltip Default
setNodeTooltipMapping Set Node Tooltip Mapping
setNodeWidthBypass Set Node Width Bypass
setNodeWidthDefault Set Node Width Default
setNodeWidthMapping Set Node Width Mapping
setNotebookIsRunning setNotebookIsRunning
setSandboxReinitialize setSandboxReinitialize
setStyleDependencies Set Style Dependencies
setVisualPropertyDefault Set Visual Property Default
setVisualStyle Set Visual Style
spoofResponse spoofResponse
spoofResponse-class spoofResponse
syncNodeCustomGraphicsSize Sync Node Custom Graphics Size

-- T --

toggleGraphicsDetails Toggle Graphics Details

-- U --

ungroupAnnotation Ungroup Annotation Group
unhideAll Unhide All
unhideEdges Unhide Edges
unhideNodes Unhide Nodes
uninstallApp Uninstall App
UpdateAnnotationBoundedText Update Bounded Text Annotation
updateAnnotationImage Update Image Annotation
updateAnnotationShape Update Shape Annotation
updateAnnotationText Update Text Annotation
updateApp Update App
updateGroupAnnotation Update Group Annotation
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

-- misc --

.exportShowImage .exportShowImage
.getDefaultSandbox .getDefaultSandbox
.getRequester .getRequester