Man pages for RCy3
Functions to Access and Control Cytoscape

addCyEdgesAdd CyEdges
addCyNodesAdd CyNodes
AddToGroupAdd to Group
applyFilterApply Filter
bundleEdgesBundle Edges
clearEdgePropertyBypassClear Edge Property Bypass
clearNetworkCenterBypassClear Network Center Bypass
clearNetworkPropertyBypassClear Network Property Bypass
clearNetworkZoomBypassClear Network Zoom Bypass
clearNodeOpacityBypassClear Node Opacity Bypass
clearNodePropertyBypassClear Node Property Bypass
clearSelectionClear Selection
cloneNetworkClone a Cytoscape Network
closeSessionClose Session
collapseGroupCollapse Group
commandEchoCommand Echo
commandOpenDialogCommand Open Dialog
commandPauseCommand Pause
commandQuitCommand Quit
commandRunFileCommand Run File
commandsAPIOpen Swagger docs for CyREST Commands API
commandsGETCommands GET
commandsHelpCommands Help
commandSleepCommand Sleep
commandsPOSTCommands POST
commandsRunRun a Command
copyCytoscapeNetwork-defunctDEFUNCT: copyCytoscapeNetwork
copyVisualStyleCopy Visual Style
createColumnFilterCreate Column Filter
createCompositeFilterCreate Composite Filter
createDegreeFilterCreate Degree Filter
createGraphFromNetworkcreateGraphFromNetwork
createGroupCreate Group
createIgraphFromNetworkCreate an igraph network from a Cytoscape network
createNetworkFromDataFramesCreate a network from data frames
createNetworkFromGraphCreate Network From Graph
createNetworkFromIgraphCreate a Cytoscape network from an igraph network
createSubnetworkCreate subnetwork from existing network
createVisualStyleCreate a visual style from components
createWindow-defunctDEFUNCT: createWindow
createWindowFromSelection-defunctDEFUNCT: createWindowFromSelection
cybrowserCloseCybrowser Close
cybrowserDialogCybrowser Dialog
cybrowserHideCybrowser Hide
cybrowserListCybrowser List
cybrowserSendCybrowser Send
cybrowserShowCybrowser Show
cybrowserVersionCybrowser Version
cyrestAPIOpen Swagger docs for CyREST API
cyrestDELETECyREST DELETE
cyrestGETCyREST GET
cyrestPOSTCyREST POST
cyrestPUTCyREST PUT
cytoscapeApiVersionsAvailable CyREST API Versions
CytoscapeConnection-defunctDEFUNCT: CytoscapeConnection
cytoscapeFreeMemoryFree Up Unused Memory for Cytoscape
cytoscapeMemoryStatusMemory Available to Cytoscape
cytoscapeNumberOfCoresNumber of Processors Available to Cytoscape
cytoscapePingPing Cytoscape
cytoscapeVersionInfoCytoscape and CyREST API Versions
CytoscapeWindow-defunctDEFUNCT: CytoscapeWindow
deleteAllNetworksDelete All Networks
deleteAllWindows-defunctDEFUNCT: deleteAllWindows
deleteDuplicateEdgesDelete Duplicate Edges
deleteEdgeAttribute-defunctDEFUNCT: deleteEdgeAttribute
deleteGroupDelete (or Ungroup) a Group
deleteNetworkDelete Network
deleteNodeAttribute-defunctDEFUNCT: deleteNodeAttribute
deleteSelectedEdgesDelete Selected Edges
deleteSelectedNodesDelete Selected Nodes
deleteSelfLoopsDelete Self Loops
deleteStyleMappingDelete Style Mapping
deleteTableColumnDelete a table column
deleteVisualStyleDelete Visual Style
deleteWindow-defunctDEFUNCT: deleteWindow
diffusionAdvancedDiffusion Advanced
diffusionBasicDiffusion Basic
disableAppDisable App
dockPanelDock Panel
enableAppEnable App
existing.CytoscapeWindow-defunctDEFUNCT: existing.CytoscapeWindow
expandGroupExpand Group
exportFiltersExport Filters
exportImageExport Image
exportNetworkExport Network
exportNetworkToNDExExport Network To NDEx
exportVisualStylesExport Visual Styles
fitContentFit Content
fitSelectedContent-defunctDEFUNCT: fitSelectedContent
floatPanelFloat Panel
getAllEdgeAttributes-defunctDEFUNCT: getAllEdgeAttributes
getAllEdgesGet All Edges
getAllNodeAttributes-defunctDEFUNCT: getAllNodeAttributes
getAllNodesGet All Nodes
getAppInformationGet App Information
getAppStatusApp Status
getAppUpdatesList Apps With Updates
getArrowShapesGet Arrow Shapes
getAvailableAppsList Available Apps
getBackgroundColorDefaultGet Background Color Default
getCenter-defunctDEFUNCT: getCenter
getCollectionListGet Collection List
getCollectionNameGet Collection Name
getCollectionNetworksGet Collection Networks
getCollectionSuidGet Collection Suid
getCommandNames-defunctDEFUNCT: getCommandNames
getCommandNamesWithinNamespace-defunctDEFUNCT: getCommandNamesWithinNamespace
getDirectlyModifiableVisualProperties-defunctDEFUNCT: getDirectlyModifiableVisualProperties
getDisabledAppsList Disabled Apps
getEdgeAttribute-defunctDEFUNCT: getEdgeAttribute
getEdgeAttributeNames-defunctDEFUNCT: getEdgeAttributeNames
getEdgeColorGet Edge Color
getEdgeCountGet Edge Count
getEdgeLineStyleGet Edge Line Style
getEdgeLineWidthGet Edge Line Width
getEdgePropertyGet Edge Property Values
getEdgeSelectionColorDefaultGet Edge Selection Color Default
getEdgeTargetArrowShapeGet Edge Target Arrow Shape
getFilterListGet Filter List
getFirstNeighborsGet list of nodes neighboring provided list
getGraphFromCyWindow-defunctDEFUNCT: getGraphFromCyWindow
getGroupInfoGet Group Information
getInstalledAppsList Installed Apps
getLayoutNameMappingGet Layout Name Mapping
getLayoutNamesGet Layout Names
getLayoutPropertyNamesGet Layout Property Names
getLayoutPropertyTypeGet Layout Property Type
getLayoutPropertyValueGet Layout Property Value
getLineStylesGet Line Styles
getNetworkCenterGet Network Center
getNetworkCountGet the number of Cytoscape networks
getNetworkListGet the list of Cytoscape networks
getNetworkNameGet the name of a network
getNetworkNDExIdGet Network NDEx Id
getNetworkPropertyGet Network Property Values
getNetworkSuidGet the SUID of a network
getNetworkViewsGet Network Views
getNetworkViewSuidGet the SUID of a network view
getNetworkZoomGet Network Zoom
getNodeAttribute-defunctDEFUNCT: getNodeAttribute
getNodeAttributeNames-defunctDEFUNCT: getNodeAttributeNames
getNodeColorGet Node Color
getNodeCountGet Node Count
getNodeHeightGet Node Height
getNodePropertyGet Node Property Values
getNodeSelectionColorDefaultGet Node Selection Color Default
getNodeShapesGet Node Shapes
getNodeSizeGet Node Size
getNodeWidthGet Node Width
getSelectedEdgeCountGet Selected Edge Count
getSelectedEdgesGet Selected Edges
getSelectedNodeCountGet Selected Node Count
getSelectedNodesGet Selected Nodes
getStyleDependenciesGet the values of dependencies in a style
getTableColumnNamesGet Table Column Names
getTableColumnsGet table column values
getTableColumnTypesGet Table Column Types
getTableValueGet table cell value
getUninstalledAppsList Uninstalled Apps
getVisualPropertyDefaultGet Visual Property Default
getVisualPropertyNamesGet Visual Property Names
getVisualStyleNamesGet Visual Style Names
getWindowCount-defunctDEFUNCT: getWindowCount
getWindowID-defunctDEFUNCT: getWindowID
getWindowList-defunctDEFUNCT: getWindowList
getZoom-defunctDEFUNCT: getZoom
hideAllPanelsHide All Panels
hideEdgesHide Edges
hideNodesHide Nodes
hidePanelHide Panel
hideSelectedEdgesHide Selected Edges
hideSelectedNodesHide Selected Nodes
importFiltersImport Filters
importNetworkFromFileImport Network From File
importNetworkFromNDExImport Network From NDEx
importVisualStylesImport Visual Styles
installAppInstall App
invertEdgeSelectionInvert Edge Selection
invertNodeSelectionInvert Node Selection
layoutCopycatCopy a layout from one network to another
layoutNetworkApply a layout to a network
listGroupsList Groups
loadTableDataLoads data into Cytoscape tables keyed by row
lockNodeDimensionsLock Node Dimensions
makeSimpleGraphMake Simple Graph
makeSimpleIgraphMake Simple Igraph
mapTableColumnMap Table Column
mapVisualPropertyCreates a mapping between an attribute and a visual property
matchArrowColorToEdgeMatch Arrow Color To Edge
openAppStoreOpen App Store Page
openSessionOpen Session File or URL
ping-defunctDEFUNCT: ping
pluginVersion-defunctDEFUNCT: pluginVersion
RCy3RCy3: Functions to Access and Control Cytoscape
redraw-defunctDEFUNCT: redraw
RemoveFromGroupRemove from Group
removeNodeCustomGraphicsRemove Node Custom Graphics
renameCytoscapeNetwork-defunctDEFUNCT: renameCytoscapeNetwork
renameNetworkRename a network
renameTableColumnRename Table Column
saveImage-defunctDEFUNCT: saveImage
saveNetwork-defunctDEFUNCT: saveNetwork
saveSessionSave Session to File
selectAllEdgesSelect all edges
selectAllNodesSelect all nodes
selectEdgesSelect Edges
selectEdgesAdjacentToSelectedNodesSelect Edges Adjacent To Selected Nodes
selectEdgesConnectedBySelectedNodes-defunctDEFUNCT: selectEdgesConnectedBySelectedNodes
selectEdgesConnectingSelectedNodesSelect the edges connecting selected nodes in Cytoscape...
selectFirstNeighborsSelect first neighbor nodes
selectFirstNeighborsOfSelectedNodes-defunctDEFUNCT: selectFirstNeighborsOfSelectedNodes
selectNodesSelect Nodes
selectNodesConnectedBySelectedEdgesSelect Nodes Connected By Selected Edges
setBackgroundColorDefaultSet Background Color Default
setCenter-defunctDEFUNCT: setCenter
setCurrentNetworkSet current network
setCurrentViewSet Current View
setEdgeColorBypassSet Edge Color Bypass
setEdgeColorDefaultSet Edge Color Default
setEdgeColorMappingSet Edge Color Mapping
setEdgeFontFaceBypassSet Edge Font Face Bypass
setEdgeFontSizeBypassSet Edge Font Size Bypass
setEdgeFontSizeDefaultSet Edge Font Size Default
setEdgeLabelBypassSet Edge Label Bypass
setEdgeLabelColorBypassSet Edge Label Color Bypass
setEdgeLabelMappingSet Edge Label Mapping
setEdgeLabelOpacityBypassSet Edge Label Opacity Bypass
setEdgeLineStyleBypassSet Edge Line Style Bypass
setEdgeLineStyleDefaultSet Edge Line Style Default
setEdgeLineStyleMappingSet Edge Line Style Mapping
setEdgeLineWidthBypassSet Edge Line Width Bypass
setEdgeLineWidthDefaultSet Edge Line Width Default
setEdgeLineWidthMappingSet Edge Line Width Mapping
setEdgeOpacityBypassSet Edge Opacity Bypass
setEdgeOpacityMappingSet Edge Opacity Mapping
setEdgePropertyBypassSet Edge Property Bypass
setEdgeSelectionColorDefaultSet Edge Selection Color Default
setEdgeSourceArrowColorBypassSet Edge Source Arrow Color Bypass
setEdgeSourceArrowColorDefaultSet Edge Source Arrow Color Default
setEdgeSourceArrowColorMappingSet Edge Source Arrow Color Mapping
setEdgeSourceArrowMappingSet Edge Source Arrow Mapping
setEdgeSourceArrowShapeBypassSet Edge Source Arrow Shape Bypass
setEdgeSourceArrowShapeDefaultSet Edge Source Arrow Shape Default
setEdgeTargetArrowColorBypassSet Edge Target Arrow Color Bypass
setEdgeTargetArrowColorDefaultSet Edge Target Arrow Color Default
setEdgeTargetArrowColorMappingSet Edge Target Arrow Color Mapping
setEdgeTargetArrowMappingSet Edge Target Arrow Mapping
setEdgeTargetArrowShapeBypassSet Edge Target Arrow Shape Bypass
setEdgeTargetArrowShapeDefaultSet Edge Target Arrow Shape Default
setEdgeTooltipBypassSet Edge Tooltip Bypass
setEdgeTooltipMappingSet Edge Tooltip Mapping
setLayoutPropertiesSet Layout Properties
setNetworkCenterBypassSet Network Center Bypass
setNetworkPropertyBypassSet Network Property Bypass
setNetworkZoomBypassSet Network Zoom Bypass
setNodeBorderColorBypassSet Node Border Color Bypass
setNodeBorderColorDefaultSet Node Border Color Default
setNodeBorderColorMappingSet Node Border Color Mapping
setNodeBorderOpacityBypassSet Node Border Opacity Bypass
setNodeBorderWidthBypassSet Node Border Width Bypass
setNodeBorderWidthDefaultSet Node Border Width Default
setNodeBorderWidthMappingSet Node Border Width Mapping
setNodeColorBypassSet Node Color Bypass
setNodeColorDefaultSet Node Color Default
setNodeColorMappingSet Node Color Mapping
setNodeComboOpacityMappingSet Node Combo Opacity Mapping
setNodeCustomBarChartSet Node Custom Bar Chart
setNodeCustomBoxChartSet Node Custom Box Chart
setNodeCustomHeatMapChartSet Node Custom HeatMap Chart
setNodeCustomLinearGradientSet Node Custom Linear Gradient
setNodeCustomLineChartSet Node Custom Line Chart
setNodeCustomPieChartSet Node Custom Pie Chart
setNodeCustomPositionSet Node Custom Position
setNodeCustomRadialGradientSet Node Custom Radial Gradient
setNodeCustomRingChartSet Node Custom Ring Chart
setNodeFillOpacityBypassSet Node Fill Opacity Bypass
setNodeFontSizeBypassSet Node Font Size Bypass
setNodeFontSizeDefaultSet Node Font Size Default
setNodeHeightBypassSet Node Height Bypass
setNodeLabelBypassSet Node Label Bypass
setNodeLabelColorBypassSet Node Label Color Bypass
setNodeLabelColorDefaultSet Node Label Color Default
setNodeLabelMappingSet Node Label Mapping
setNodeLabelOpacityBypassSet Node Label Opacity Bypass
setNodeOpacityBypassSet Node Opacity Bypass
setNodePropertyBypassSet Node Property Bypass
setNodeSelectionColorDefaultSet Node Selection Color Default
setNodeShapeBypassSet Node Shape Bypass
setNodeShapeDefaultSet Node Shape Default
setNodeShapeMappingSet Node Shape Mapping
setNodeSizeBypassSet Node Size Bypass
setNodeSizeDefaultSet Node Size Default
setNodeSizeMappingSet Node Size Mapping
setNodeTooltipMappingSet Node Tooltip Mapping
setNodeWidthBypassSet Node Width Bypass
setStyleDependenciesSet Style Dependencies
setVisualPropertyDefaultSet Visual Property Default
setVisualStyleSet Visual Style
setZoom-defunctDEFUNCT: setZoom
sfn-defunctDEFUNCT: sfn
showGraphicsDetails-defunctDEFUNCT: showGraphicsDetails
syncNodeCustomGraphicsSizeSync Node Custom Graphics Size
toggleGraphicsDetailsToggle Graphics Details
unhideAllUnhide All
unhideEdgesUnhide Edges
unhideNodesUnhide Nodes
uninstallAppUninstall App
updateAppUpdate App
updateNetworkInNDExUpdate Network In NDEx
updateStyleDefaultsUpdates the default values of visual properties in a style
updateStyleMappingUpdates a visual property mapping in a style
RCy3 documentation built on Dec. 8, 2018, 6 p.m.