# Functions to Access and Control Cytoscape

## Documentation for package ‘RCy3’ version 2.33.0

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

## Help Pages

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

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

## -- 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
createCytoscapejsFromNetwork | Create Cytoscapejs from Network
createDegreeFilter | Create Degree Filter
createGraphFromNetwork | createGraphFromNetwork
createGroup | Create Group
createGroupByColumn | Create Group by Column
createIgraphFromNetwork | Create an igraph network from a Cytoscape network
createNetworkFromCytoscapejs | Create a Network from Cytoscapejs
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
createView | Create Network View
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
deleteAllVisualStyle | Delete All Visual Style
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
exportJPG | Export JPG
exportNetwork | Export Network
exportNetworkToNDEx | Export Network To NDEx
exportPDF | Export PDF
exportPNG | Export PNG
exportPS | Export PS
exportSVG | Export SVG
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
getNodeLabelPosition | Get Node Label Position
getNodeLabelPositionDefault | Get Node Label Position Default
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
getVisualStyleJSON | Get Visual Style JSON
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 --

importFileFromUrl | importFileFromUrl
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
paletteColorVirdis | paletteColorVirdis

## -- 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
rotateLayout | Rotate Layout
runningRemoteCheck | runningRmoteCheck

## -- S --

sandboxGetFileInfo | sandboxGetFileInfo
sandboxGetFrom | sandboxGetFrom
sandboxInitializer | sandboxInitializer
sandboxRemove | sandboxRemove
sandboxRemoveFile | sandboxRemoveFile
sandboxSendTo | sandboxSendTo
sandboxSet | sandboxSet
sandboxUrlTo | sandboxUrlTo
saveSession | Save Session to File
scaleLayout | Scale Layout
selectAll | Select all nodes and edges
selectAllEdges | Select all edges
selectAllNodes | Select all nodes
selectEdges | Select Edges
selectEdgesAdjacentToNodes | Select Edges Adjacent To Nodes
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
setCollectionName | Set Collection Name
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
setNodeLabelPositionBypass | Set Node Label Position Bypass
setNodeLabelPositionDefault | Set Node Label Position Default
setNodeOpacityBypass | Set Node Opacity Bypass
setNodePositionBypass | Set Node Position 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