Functions to Access and Control Cytoscape
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Documentation for package ‘RCy3’ version 2.14.2
Help Pages
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 |