Package: RCy3 2.27.0

Alex Pico

RCy3: Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Authors:Alex Pico [aut, cre], Tanja Muetze [aut], Paul Shannon [aut], Ruth Isserlin [ctb], Shraddha Pai [ctb], Julia Gustavsen [ctb], Georgi Kolishovski [ctb], Yihang Xin [ctb]

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RCy3.pdf |RCy3.html✨
RCy3/json (API)
NEWS

# Install 'RCy3' in R:

install.packages('RCy3', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cytoscape/rcy3/issues

On BioConductor:RCy3-2.27.0(bioc 3.21)RCy3-2.26.0(bioc 3.20)

visualization graphandnetwork thirdpartyclient network

13.39 score 52 stars 16 packages 600 scripts 1.5k downloads 22 mentions 416 exports 42 dependencies

Last updated 2 months agofrom:6d1a209939. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	NOTE	Dec 19 2024
R-4.5-linux	NOTE	Dec 19 2024
R-4.4-win	NOTE	Dec 19 2024
R-4.4-mac	NOTE	Dec 19 2024
R-4.3-win	NOTE	Dec 19 2024
R-4.3-mac	NOTE	Dec 19 2024

Exports:addAnnotationBoundedText addAnnotationImage addAnnotationShape addAnnotationText addCyEdges addCyNodes AddToGroup analyzeNetwork applyFilter bundleEdges checkNotebookIsRunning checkRunningRemote clearEdgeBends clearEdgePropertyBypass clearNetworkCenterBypass clearNetworkPropertyBypass clearNetworkZoomBypass clearNodeOpacityBypass clearNodePropertyBypass clearSelection cloneNetwork closeSession collapseGroup commandEcho commandOpenDialog commandPause commandQuit commandRunFile commandsAPI commandsGET commandsHelp commandSleep commandsPOST commandsRun copyVisualStyle createColumnFilter createCompositeFilter createCytoscapejsFromNetwork createDegreeFilter createGraphFromNetwork createGroup createGroupByColumn createIgraphFromNetwork createNetworkFromCytoscapejs createNetworkFromDataFrames createNetworkFromGraph createNetworkFromIgraph createSubnetwork createView createVisualStyle cybrowserClose cybrowserDialog cybrowserHide cybrowserList cybrowserSend cybrowserShow cybrowserVersion cyrestAPI cyrestDELETE cyrestGET cyrestPOST cyrestPUT cytoscapeApiVersions cytoscapeFreeMemory cytoscapeMemoryStatus cytoscapeNumberOfCores cytoscapePing cytoscapeVersionInfo deleteAllNetworks deleteAllVisualStyle deleteAnnotation deleteDuplicateEdges deleteGroup deleteNetwork deleteSelectedEdges deleteSelectedNodes deleteSelfLoops deleteStyleMapping deleteTableColumn deleteVisualStyle diffusionAdvanced diffusionBasic disableApp dockPanel doInitializeSandbox doRequestRemote doSetSandbox enableApp expandGroup exportFilters exportImage exportJPG exportNetwork exportNetworkToNDEx exportPDF exportPNG exportPS exportSVG exportVisualStyles findRemoteCytoscape fitContent floatPanel getAbsSandboxPath getAllEdges getAllNodes getAllStyleMappings getAnnotationList getAppInformation getAppStatus getAppUpdates getArrowShapes getAvailableApps getBackgroundColorDefault getBrowserClientChannel getBrowserClientJs getCollectionList getCollectionName getCollectionNetworks getCollectionSuid getCurrentSandbox getCurrentSandboxName getCurrentSandboxPath getCurrentStyle getDefaultSandbox getDefaultSandboxPath getDisabledApps getEdgeColor getEdgeCount getEdgeInfo getEdgeLineStyle getEdgeLineWidth getEdgeProperty getEdgeSelectionColorDefault getEdgeTargetArrowShape getFilterList getFirstNeighbors getGroupInfo getInstalledApps getJupyterBridgeURL getLayoutNameMapping getLayoutNames getLayoutPropertyNames getLayoutPropertyType getLayoutPropertyValue getLineStyles getNetworkCenter getNetworkCount getNetworkList getNetworkName getNetworkNDExId getNetworkProperty getNetworkSuid getNetworkViews getNetworkViewSuid getNetworkZoom getNodeColor getNodeCount getNodeHeight getNodeLabelPosition getNodeLabelPositionDefault getNodePosition getNodeProperty getNodeSelectionColorDefault getNodeShapes getNodeSize getNodeWidth getNotebookIsRunning getSandboxReinitialize getSelectedEdgeCount getSelectedEdges getSelectedNodeCount getSelectedNodes getStyleDependencies getStyleMapping getTableColumnNames getTableColumns getTableColumnTypes getTableValue getUninstalledApps getVisualPropertyDefault getVisualPropertyNames getVisualStyleJSON getVisualStyleNames groupAnnotation hideAllPanels hideEdges hideNodes hidePanel hideSelectedEdges hideSelectedNodes importFileFromUrl importFilters importNetworkFromFile importNetworkFromNDEx importVisualStyles installApp invertEdgeSelection invertNodeSelection layoutCopycat layoutNetwork listGroups loadTableData lockNodeDimensions makeSimpleGraph makeSimpleIgraph mapTableColumn mapVisualProperty matchArrowColorToEdge mergeNetworks notebookExportShowImage notebookShowImage openAppStore openSession paletteColorBrewerAccent paletteColorBrewerBlues paletteColorBrewerBrBG paletteColorBrewerBuGn paletteColorBrewerBuPu paletteColorBrewerDark2 paletteColorBrewerGnBu paletteColorBrewerGreens paletteColorBrewerGreys paletteColorBrewerOranges paletteColorBrewerOrRd paletteColorBrewerPaired paletteColorBrewerPastel1 paletteColorBrewerPastel2 paletteColorBrewerPiYG paletteColorBrewerPRGn paletteColorBrewerPuBu paletteColorBrewerPuBuGn paletteColorBrewerPuOr paletteColorBrewerPuRd paletteColorBrewerPurples paletteColorBrewerRdBu paletteColorBrewerRdPu paletteColorBrewerRdYlBu paletteColorBrewerReds paletteColorBrewerSet1 paletteColorBrewerSet2 paletteColorBrewerSet3 paletteColorBrewerYlGn paletteColorBrewerYlGnBu paletteColorBrewerYlOrBr paletteColorBrewerYlOrRd paletteColorRandom paletteColorVirdis RemoveFromGroup removeNodeCustomGraphics renameNetwork renameTableColumn resetDefaultSandbox rotateLayout runningRemoteCheck sandboxGetFileInfo sandboxGetFrom sandboxInitializer sandboxRemove sandboxRemoveFile sandboxSendTo sandboxSet sandboxUrlTo saveSession scaleLayout selectAll selectAllEdges selectAllNodes selectEdges selectEdgesAdjacentToNodes selectEdgesAdjacentToSelectedNodes selectEdgesConnectingSelectedNodes selectFirstNeighbors selectNodes selectNodesConnectedBySelectedEdges setBackgroundColorDefault setCatchupFilterSecs setCatchupNetworkSecs setCurrentNetwork setCurrentSandbox setCurrentView setDefaultSandbox setDefaultSandboxPath setEdgeColorBypass setEdgeColorDefault setEdgeColorMapping setEdgeFontFaceBypass setEdgeFontFaceDefault setEdgeFontFaceMapping setEdgeFontSizeBypass setEdgeFontSizeDefault setEdgeFontSizeMapping setEdgeLabelBypass setEdgeLabelColorBypass setEdgeLabelColorDefault setEdgeLabelColorMapping setEdgeLabelDefault setEdgeLabelMapping setEdgeLabelOpacityBypass setEdgeLabelOpacityDefault setEdgeLabelOpacityMapping setEdgeLineStyleBypass setEdgeLineStyleDefault setEdgeLineStyleMapping setEdgeLineWidthBypass setEdgeLineWidthDefault setEdgeLineWidthMapping setEdgeOpacityBypass setEdgeOpacityDefault setEdgeOpacityMapping setEdgePropertyBypass setEdgeSelectionColorDefault setEdgeSourceArrowColorBypass setEdgeSourceArrowColorDefault setEdgeSourceArrowColorMapping setEdgeSourceArrowMapping setEdgeSourceArrowShapeBypass setEdgeSourceArrowShapeDefault setEdgeSourceArrowShapeMapping setEdgeTargetArrowColorBypass setEdgeTargetArrowColorDefault setEdgeTargetArrowColorMapping setEdgeTargetArrowMapping setEdgeTargetArrowShapeBypass setEdgeTargetArrowShapeDefault setEdgeTargetArrowShapeMapping setEdgeTooltipBypass setEdgeTooltipDefault setEdgeTooltipMapping setLayoutProperties setModelPropagationSecs setNetworkCenterBypass setNetworkPropertyBypass setNetworkZoomBypass setNodeBorderColorBypass setNodeBorderColorDefault setNodeBorderColorMapping setNodeBorderOpacityBypass setNodeBorderOpacityDefault setNodeBorderOpacityMapping setNodeBorderWidthBypass setNodeBorderWidthDefault setNodeBorderWidthMapping setNodeColorBypass setNodeColorDefault setNodeColorMapping setNodeComboOpacityMapping setNodeCustomBarChart setNodeCustomBoxChart setNodeCustomHeatMapChart setNodeCustomLinearGradient setNodeCustomLineChart setNodeCustomPieChart setNodeCustomPosition setNodeCustomRadialGradient setNodeCustomRingChart setNodeFillOpacityBypass setNodeFillOpacityDefault setNodeFillOpacityMapping setNodeFontFaceBypass setNodeFontFaceDefault setNodeFontFaceMapping setNodeFontSizeBypass setNodeFontSizeDefault setNodeFontSizeMapping setNodeHeightBypass setNodeHeightDefault setNodeHeightMapping setNodeLabelBypass setNodeLabelColorBypass setNodeLabelColorDefault setNodeLabelColorMapping setNodeLabelDefault setNodeLabelMapping setNodeLabelOpacityBypass setNodeLabelOpacityDefault setNodeLabelOpacityMapping setNodeLabelPositionBypass setNodeLabelPositionDefault setNodeOpacityBypass setNodePositionBypass setNodePropertyBypass setNodeSelectionColorDefault setNodeShapeBypass setNodeShapeDefault setNodeShapeMapping setNodeSizeBypass setNodeSizeDefault setNodeSizeMapping setNodeTooltipBypass setNodeTooltipDefault setNodeTooltipMapping setNodeWidthBypass setNodeWidthDefault setNodeWidthMapping setNotebookIsRunning setSandboxReinitialize setStyleDependencies setVisualPropertyDefault setVisualStyle spoofResponse syncNodeCustomGraphicsSize toggleGraphicsDetails ungroupAnnotation unhideAll unhideEdges unhideNodes uninstallApp UpdateAnnotationBoundedText updateAnnotationImage updateAnnotationShape updateAnnotationText updateApp updateGroupAnnotation updateNetworkInNDEx updateStyleDefaults updateStyleMapping

Dependencies:askpass backports base64enc base64url BiocGenerics bitops caTools cli crayon curl digest evaluate fastmap fs generics glue gplots graph gtools htmltools httr IRdisplay IRkernel jsonlite KernSmooth lifecycle mime openssl pbdZMQ pillar R6 RColorBrewer RCurl repr RJSONIO rlang stringi sys utf8 uuid vctrs XML

Overview of RCy3

by Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Rendered fromOverview-of-RCy3.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2019-09-28
Started: 2018-03-18

Cytoscape and igraph

by Alexander Pico

Rendered fromCytoscape-and-iGraph.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-07-14
Started: 2018-03-18

Cytoscape and graphNEL

by Alexander Pico

Rendered fromCytoscape-and-graphNEL.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-06-24
Started: 2018-02-18

Importing data

by Alexander Pico

Rendered fromImporting-data.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-06-24
Started: 2018-01-14

Network functions and visualization

by Alexander Pico

Rendered fromNetwork-functions-and-visualization.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-06-25
Started: 2018-03-16

Cancer networks and data

by Alexander Pico

Rendered fromCancer-networks-and-data.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2021-09-27
Started: 2018-03-16

Identifier mapping

by Alexander Pico

Rendered fromIdentifier-mapping.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-04-05
Started: 2018-04-07

Upgrading existing scripts

by Alexander Pico, Tanja Muetze, Paul Shannon

Rendered fromUpgrading-existing-scripts.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-07-14
Started: 2018-04-08

Cytoscape and NDEx

by Alexander Pico, Florian Auer

Rendered fromCytoscape-and-NDEx.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-06-29
Started: 2018-04-22

Group nodes

by Mark Grimes

Rendered fromGroup-nodes.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-07-14
Started: 2018-06-24

Custom Graphics and Labels

Kristina Hanspers, Alexander Pico

Rendered fromCustom-Graphics.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-11-18
Started: 2018-11-17

Filtering Networks

Kristina Hanspers, Alexander Pico

Rendered fromFiltering-Networks.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2019-12-05
Started: 2018-11-28

Phylogenetic-trees

Alexander Pico, Gildas Lepennetier

Rendered fromPhylogenetic-trees.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2019-03-08
Started: 2019-03-08

Jupyter Bridge and RCy3

by Yihang Xin and Alexander Pico

Rendered fromJupyter-bridge-rcy3.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2022-04-07
Started: 2022-04-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
.exportShowImage	.exportShowImage
.getDefaultSandbox	.getDefaultSandbox
.getRequester	.getRequester
Add Bounded Text Annotation	addAnnotationBoundedText
Add Image Annotation	addAnnotationImage
Add Shape Annotation	addAnnotationShape
Add Text Annotation	addAnnotationText
Add CyEdges	addCyEdges
Add CyNodes	addCyNodes
Add to Group	AddToGroup
Analyze Network	analyzeNetwork
Apply Filter	applyFilter
Bundle Edges	bundleEdges
checkNotebookIsRunning	checkNotebookIsRunning
checkRunningRemote	checkRunningRemote
Clear Edge Bends	clearEdgeBends
Clear Edge Property Bypass	clearEdgePropertyBypass
Clear Network Center Bypass	clearNetworkCenterBypass
Clear Network Property Bypass	clearNetworkPropertyBypass
Clear Network Zoom Bypass	clearNetworkZoomBypass
Clear Node Opacity Bypass	clearNodeOpacityBypass
Clear Node Property Bypass	clearNodePropertyBypass
Clear Selection	clearSelection
Clone a Cytoscape Network	cloneNetwork
Close Session	closeSession
Collapse Group	collapseGroup
Command Echo	commandEcho
Command Open Dialog	commandOpenDialog
Command Pause	commandPause
Command Quit	commandQuit
Command Run File	commandRunFile
Open Swagger docs for CyREST Commands API	commandsAPI
Commands GET	commandsGET
Commands Help	commandsHelp
Command Sleep	commandSleep
Commands POST	commandsPOST
Run a Command	commandsRun
Copy Visual Style	copyVisualStyle
Create Column Filter	createColumnFilter
Create Composite Filter	createCompositeFilter
Create Cytoscapejs from Network	createCytoscapejsFromNetwork
Create Degree Filter	createDegreeFilter
createGraphFromNetwork	createGraphFromNetwork
Create Group	createGroup
Create Group by Column	createGroupByColumn
Create an igraph network from a Cytoscape network	createIgraphFromNetwork
Create a Network from Cytoscapejs	createNetworkFromCytoscapejs
Create a network from data frames	createNetworkFromDataFrames
Create Network From Graph	createNetworkFromGraph
Create a Cytoscape network from an igraph network	createNetworkFromIgraph
Create subnetwork from existing network	createSubnetwork
Create Network View	createView
Create a visual style from components	createVisualStyle
Cybrowser Close	cybrowserClose
Cybrowser Dialog	cybrowserDialog
Cybrowser Hide	cybrowserHide
Cybrowser List	cybrowserList
Cybrowser Send	cybrowserSend
Cybrowser Show	cybrowserShow
Cybrowser Version	cybrowserVersion
Open Swagger docs for CyREST API	cyrestAPI
CyREST DELETE	cyrestDELETE
CyREST GET	cyrestGET
CyREST POST	cyrestPOST
CyREST PUT	cyrestPUT
Available CyREST API Versions	cytoscapeApiVersions
Free Up Unused Memory for Cytoscape	cytoscapeFreeMemory
Memory Available to Cytoscape	cytoscapeMemoryStatus
Number of Processors Available to Cytoscape	cytoscapeNumberOfCores
Ping Cytoscape	cytoscapePing
Cytoscape and CyREST API Versions	cytoscapeVersionInfo
Delete All Networks	deleteAllNetworks
Delete All Visual Style	deleteAllVisualStyle
Delete Annotation	deleteAnnotation
Delete Duplicate Edges	deleteDuplicateEdges
Delete (or Ungroup) a Group	deleteGroup
Delete Network	deleteNetwork
Delete Selected Edges	deleteSelectedEdges
Delete Selected Nodes	deleteSelectedNodes
Delete Self Loops	deleteSelfLoops
Delete Style Mapping	deleteStyleMapping
Delete a table column	deleteTableColumn
Delete Visual Style	deleteVisualStyle
Diffusion Advanced	diffusionAdvanced
Diffusion Basic	diffusionBasic
Disable App	disableApp
Dock Panel	dockPanel
doInitializeSandbox	doInitializeSandbox
doRequestRemote	doRequestRemote
doSetSandbox	doSetSandbox
Enable App	enableApp
Expand Group	expandGroup
Export Filters	exportFilters
Export Image	exportImage
Export JPG	exportJPG
Export Network	exportNetwork
Export Network To NDEx	exportNetworkToNDEx
Export PDF	exportPDF
Export PNG	exportPNG
Export PS	exportPS
Export SVG	exportSVG
Export Visual Styles	exportVisualStyles
findRemoteCytoscape	findRemoteCytoscape
Fit Content	fitContent
Float Panel	floatPanel
getAbsSandboxPath	getAbsSandboxPath
Get All Edges	getAllEdges
Get All Nodes	getAllNodes
Get All Style Mappings	getAllStyleMappings
Get Annotation List	getAnnotationList
Get App Information	getAppInformation
App Status	getAppStatus
List Apps With Updates	getAppUpdates
Get Arrow Shapes	getArrowShapes
List Available Apps	getAvailableApps
Get Background Color Default	getBackgroundColorDefault
getBrowserClientChannel	getBrowserClientChannel
getBrowserClientJs	getBrowserClientJs
Get Collection List	getCollectionList
Get Collection Name	getCollectionName
Get Collection Networks	getCollectionNetworks
Get Collection Suid	getCollectionSuid
getCurrentSandbox	getCurrentSandbox
getCurrentSandboxName	getCurrentSandboxName
getCurrentSandboxPath	getCurrentSandboxPath
Get Current Style	getCurrentStyle
getDefaultSandbox	getDefaultSandbox
getDefaultSandboxPath	getDefaultSandboxPath
List Disabled Apps	getDisabledApps
Get Edge Color	getEdgeColor
Get Edge Count	getEdgeCount
Get Edge Information	getEdgeInfo
Get Edge Line Style	getEdgeLineStyle
Get Edge Line Width	getEdgeLineWidth
Get Edge Property Values	getEdgeProperty
Get Edge Selection Color Default	getEdgeSelectionColorDefault
Get Edge Target Arrow Shape	getEdgeTargetArrowShape
Get Filter List	getFilterList
Get list of nodes neighboring provided list	getFirstNeighbors
Get Group Information	getGroupInfo
List Installed Apps	getInstalledApps
getJupyterBridgeURL	getJupyterBridgeURL
Get Layout Name Mapping	getLayoutNameMapping
Get Layout Names	getLayoutNames
Get Layout Property Names	getLayoutPropertyNames
Get Layout Property Type	getLayoutPropertyType
Get Layout Property Value	getLayoutPropertyValue
Get Line Styles	getLineStyles
Get Network Center	getNetworkCenter
Get the number of Cytoscape networks	getNetworkCount
Get the list of Cytoscape networks	getNetworkList
Get the name of a network	getNetworkName
Get Network NDEx Id	getNetworkNDExId
Get Network Property Values	getNetworkProperty
Get the SUID of a network	getNetworkSuid
Get Network Views	getNetworkViews
Get the SUID of a network view	getNetworkViewSuid
Get Network Zoom	getNetworkZoom
Get Node Color	getNodeColor
Get Node Count	getNodeCount
Get Node Height	getNodeHeight
Get Node Label Position	getNodeLabelPosition
Get Node Label Position Default	getNodeLabelPositionDefault
Get Node Position	getNodePosition
Get Node Property Values	getNodeProperty
Get Node Selection Color Default	getNodeSelectionColorDefault
Get Node Shapes	getNodeShapes
Get Node Size	getNodeSize
Get Node Width	getNodeWidth
getNotebookIsRunning	getNotebookIsRunning
getSandboxReinitialize	getSandboxReinitialize
Get Selected Edge Count	getSelectedEdgeCount
Get Selected Edges	getSelectedEdges
Get Selected Node Count	getSelectedNodeCount
Get Selected Nodes	getSelectedNodes
Get the values of dependencies in a style	getStyleDependencies
Get Style Mapping	getStyleMapping
Get Table Column Names	getTableColumnNames
Get table column values	getTableColumns
Get Table Column Types	getTableColumnTypes
Get table cell value	getTableValue
List Uninstalled Apps	getUninstalledApps
Get Visual Property Default	getVisualPropertyDefault
Get Visual Property Names	getVisualPropertyNames
Get Visual Style JSON	getVisualStyleJSON
Get Visual Style Names	getVisualStyleNames
Group Annotation	groupAnnotation
Hide All Panels	hideAllPanels
Hide Edges	hideEdges
Hide Nodes	hideNodes
Hide Panel	hidePanel
Hide Selected Edges	hideSelectedEdges
Hide Selected Nodes	hideSelectedNodes
importFileFromUrl	importFileFromUrl
Import Filters	importFilters
Import Network From File	importNetworkFromFile
Import Network From NDEx	importNetworkFromNDEx
Import Visual Styles	importVisualStyles
Install App	installApp
Invert Edge Selection	invertEdgeSelection
Invert Node Selection	invertNodeSelection
Copy a layout from one network to another	layoutCopycat
Apply a layout to a network	layoutNetwork
List Groups	listGroups
Loads data into Cytoscape tables keyed by row	loadTableData
Lock Node Dimensions	lockNodeDimensions
Make Simple Graph	makeSimpleGraph
Make Simple Igraph	makeSimpleIgraph
Map Table Column	mapTableColumn
Creates a mapping between an attribute and a visual property	mapVisualProperty
Match Arrow Color To Edge	matchArrowColorToEdge
Merge Networks	mergeNetworks
notebookExportShowImage	notebookExportShowImage
notebookShowImage	notebookShowImage
Open App Store Page	openAppStore
Open Session File or URL	openSession
paletteColorBrewerAccent Qualitative	paletteColorBrewerAccent
paletteColorBrewerBlues Sequential	paletteColorBrewerBlues
paletteColorBrewerBrBG Divergent	paletteColorBrewerBrBG
paletteColorBrewerBuGn Sequential	paletteColorBrewerBuGn
paletteColorBrewerBuPu Sequential	paletteColorBrewerBuPu
paletteColorBrewerDark2 Qualitative	paletteColorBrewerDark2
paletteColorBrewerGnBu Sequential	paletteColorBrewerGnBu
paletteColorBrewerGreens Sequential	paletteColorBrewerGreens
paletteColorBrewerGreys Sequential	paletteColorBrewerGreys
paletteColorBrewerOranges Sequential	paletteColorBrewerOranges
paletteColorBrewerOrRd Sequential	paletteColorBrewerOrRd
paletteColorBrewerPaired Qualitative	paletteColorBrewerPaired
paletteColorBrewerPastel1 Qualitative	paletteColorBrewerPastel1
paletteColorBrewerPastel2 Qualitative	paletteColorBrewerPastel2
paletteColorBrewerPiYG Divergent	paletteColorBrewerPiYG
paletteColorBrewerPRGn Divergent	paletteColorBrewerPRGn
paletteColorBrewerPuBu Sequential	paletteColorBrewerPuBu
paletteColorBrewerPuBuGn Sequential	paletteColorBrewerPuBuGn
paletteColorBrewerPuOr Divergent	paletteColorBrewerPuOr
paletteColorBrewerPuRd Sequential	paletteColorBrewerPuRd
paletteColorBrewerPurples Sequential	paletteColorBrewerPurples
paletteColorBrewerRdBu Divergent	paletteColorBrewerRdBu
paletteColorBrewerRdPu Sequential	paletteColorBrewerRdPu
paletteColorBrewerRdYlBu Divergent	paletteColorBrewerRdYlBu
paletteColorBrewerReds Sequential	paletteColorBrewerReds
paletteColorBrewerSet1 Qualitative	paletteColorBrewerSet1
paletteColorBrewerSet2 Qualitative	paletteColorBrewerSet2
paletteColorBrewerSet3 Qualitative	paletteColorBrewerSet3
paletteColorBrewerYlGn Sequential	paletteColorBrewerYlGn
paletteColorBrewerYlGnBu Sequential	paletteColorBrewerYlGnBu
paletteColorBrewerYlOrBr Sequential	paletteColorBrewerYlOrBr
paletteColorBrewerYlOrRd Sequential	paletteColorBrewerYlOrRd
paletteColorRandom Qualitative	paletteColorRandom
paletteColorVirdis	paletteColorVirdis
RCy3: Functions to Access and Control Cytoscape	RCy3-package RCy3
Remove from Group	RemoveFromGroup
Remove Node Custom Graphics	removeNodeCustomGraphics
Rename a network	renameNetwork
Rename Table Column	renameTableColumn
resetDefaultSandbox	resetDefaultSandbox
Rotate Layout	rotateLayout
runningRmoteCheck	runningRemoteCheck
sandboxGetFileInfo	sandboxGetFileInfo
sandboxGetFrom	sandboxGetFrom
sandboxInitializer	sandboxInitializer
sandboxRemove	sandboxRemove
sandboxRemoveFile	sandboxRemoveFile
sandboxSendTo	sandboxSendTo
sandboxSet	sandboxSet
sandboxUrlTo	sandboxUrlTo
Save Session to File	saveSession
Scale Layout	scaleLayout
Select all nodes and edges	selectAll
Select all edges	selectAllEdges
Select all nodes	selectAllNodes
Select Edges	selectEdges
Select Edges Adjacent To Nodes	selectEdgesAdjacentToNodes
Select Edges Adjacent To Selected Nodes	selectEdgesAdjacentToSelectedNodes
Select the edges connecting selected nodes in Cytoscape Network	selectEdgesConnectingSelectedNodes
Select first neighbor nodes	selectFirstNeighbors
Select Nodes	selectNodes
Select Nodes Connected By Selected Edges	selectNodesConnectedBySelectedEdges
Set Background Color Default	setBackgroundColorDefault
Set Catchup Filter Delay	setCatchupFilterSecs
Set Catchup Network Delay	setCatchupNetworkSecs
Set current network	setCurrentNetwork
setCurrentSandbox	setCurrentSandbox
Set Current View	setCurrentView
setDefaultSandbox	setDefaultSandbox
setDefaultSandboxPath	setDefaultSandboxPath
Set Edge Color Bypass	setEdgeColorBypass
Set Edge Color Default	setEdgeColorDefault
Set Edge Color Mapping	setEdgeColorMapping
Set Edge Font Face Bypass	setEdgeFontFaceBypass
Set Edge Font Face Default	setEdgeFontFaceDefault
Set Edge Font Face Mapping	setEdgeFontFaceMapping
Set Edge Font Size Bypass	setEdgeFontSizeBypass
Set Edge Font Size Default	setEdgeFontSizeDefault
Set Edge Font Size Mapping	setEdgeFontSizeMapping
Set Edge Label Bypass	setEdgeLabelBypass
Set Edge Label Color Bypass	setEdgeLabelColorBypass
Set Edge Label Color Default	setEdgeLabelColorDefault
Set Edge Label Color Mapping	setEdgeLabelColorMapping
Set Edge Label Default	setEdgeLabelDefault
Set Edge Label Mapping	setEdgeLabelMapping
Set Edge Label Opacity Bypass	setEdgeLabelOpacityBypass
Set Edge Label Opacity Default	setEdgeLabelOpacityDefault
Set Edge Label Opacity Mapping	setEdgeLabelOpacityMapping
Set Edge Line Style Bypass	setEdgeLineStyleBypass
Set Edge Line Style Default	setEdgeLineStyleDefault
Set Edge Line Style Mapping	setEdgeLineStyleMapping
Set Edge Line Width Bypass	setEdgeLineWidthBypass
Set Edge Line Width Default	setEdgeLineWidthDefault
Set Edge Line Width Mapping	setEdgeLineWidthMapping
Set Edge Opacity Bypass	setEdgeOpacityBypass
Set Edge Opacity Default	setEdgeOpacityDefault
Set Edge Opacity Mapping	setEdgeOpacityMapping
Set Edge Property Bypass	setEdgePropertyBypass
Set Edge Selection Color Default	setEdgeSelectionColorDefault
Set Edge Source Arrow Color Bypass	setEdgeSourceArrowColorBypass
Set Edge Source Arrow Color Default	setEdgeSourceArrowColorDefault
Set Edge Source Arrow Color Mapping	setEdgeSourceArrowColorMapping
Set Edge Source Arrow Mapping	setEdgeSourceArrowMapping
Set Edge Source Arrow Shape Bypass	setEdgeSourceArrowShapeBypass
Set Edge Source Arrow Shape Default	setEdgeSourceArrowShapeDefault
Set Edge Source Arrow Shape Mapping	setEdgeSourceArrowShapeMapping
Set Edge Target Arrow Color Bypass	setEdgeTargetArrowColorBypass
Set Edge Target Arrow Color Default	setEdgeTargetArrowColorDefault
Set Edge Target Arrow Color Mapping	setEdgeTargetArrowColorMapping
Set Edge Target Arrow Mapping	setEdgeTargetArrowMapping
Set Edge Target Arrow Shape Bypass	setEdgeTargetArrowShapeBypass
Set Edge Target Arrow Shape Default	setEdgeTargetArrowShapeDefault
Set Edge Target Arrow Shape Mapping	setEdgeTargetArrowShapeMapping
Set Edge Tooltip Bypass	setEdgeTooltipBypass
Set Edge Tooltip Default	setEdgeTooltipDefault
Set Edge Tooltip Mapping	setEdgeTooltipMapping
Set Layout Properties	setLayoutProperties
Set Model Propagation Delay	setModelPropagationSecs
Set Network Center Bypass	setNetworkCenterBypass
Set Network Property Bypass	setNetworkPropertyBypass
Set Network Zoom Bypass	setNetworkZoomBypass
Set Node Border Color Bypass	setNodeBorderColorBypass
Set Node Border Color Default	setNodeBorderColorDefault
Set Node Border Color Mapping	setNodeBorderColorMapping
Set Node Border Opacity Bypass	setNodeBorderOpacityBypass
Set Node Border Opacity Default	setNodeBorderOpacityDefault
Set Node Border Opacity Mapping	setNodeBorderOpacityMapping
Set Node Border Width Bypass	setNodeBorderWidthBypass
Set Node Border Width Default	setNodeBorderWidthDefault
Set Node Border Width Mapping	setNodeBorderWidthMapping
Set Node Color Bypass	setNodeColorBypass
Set Node Color Default	setNodeColorDefault
Set Node Color Mapping	setNodeColorMapping
Set Node Combo Opacity Mapping	setNodeComboOpacityMapping
Set Node Custom Bar Chart	setNodeCustomBarChart
Set Node Custom Box Chart	setNodeCustomBoxChart
Set Node Custom HeatMap Chart	setNodeCustomHeatMapChart
Set Node Custom Linear Gradient	setNodeCustomLinearGradient
Set Node Custom Line Chart	setNodeCustomLineChart
Set Node Custom Pie Chart	setNodeCustomPieChart
Set Node Custom Position	setNodeCustomPosition
Set Node Custom Radial Gradient	setNodeCustomRadialGradient
Set Node Custom Ring Chart	setNodeCustomRingChart
Set Node Fill Opacity Bypass	setNodeFillOpacityBypass
Set Node Fill Opacity Default	setNodeFillOpacityDefault
Set Node Fill Opacity Mapping	setNodeFillOpacityMapping
Set Node Font Face Bypass	setNodeFontFaceBypass
Set Node Font Face Default	setNodeFontFaceDefault
Set Node Font Face Mapping	setNodeFontFaceMapping
Set Node Font Size Bypass	setNodeFontSizeBypass
Set Node Font Size Default	setNodeFontSizeDefault
Set Node Font Size Mapping	setNodeFontSizeMapping
Set Node Height Bypass	setNodeHeightBypass
Set Node Height Default	setNodeHeightDefault
Set Node Height Mapping	setNodeHeightMapping
Set Node Label Bypass	setNodeLabelBypass
Set Node Label Color Bypass	setNodeLabelColorBypass
Set Node Label Color Default	setNodeLabelColorDefault
Set Node Label Color Mapping	setNodeLabelColorMapping
Set Node Label Default	setNodeLabelDefault
Set Node Label Mapping	setNodeLabelMapping
Set Node Label Opacity Bypass	setNodeLabelOpacityBypass
Set Node Label Opacity Default	setNodeLabelOpacityDefault
Set Node Label Opacity Mapping	setNodeLabelOpacityMapping
Set Node Label Position Bypass	setNodeLabelPositionBypass
Set Node Label Position Default	setNodeLabelPositionDefault
Set Node Opacity Bypass	setNodeOpacityBypass
Set Node Position Bypass	setNodePositionBypass
Set Node Property Bypass	setNodePropertyBypass
Set Node Selection Color Default	setNodeSelectionColorDefault
Set Node Shape Bypass	setNodeShapeBypass
Set Node Shape Default	setNodeShapeDefault
Set Node Shape Mapping	setNodeShapeMapping
Set Node Size Bypass	setNodeSizeBypass
Set Node Size Default	setNodeSizeDefault
Set Node Size Mapping	setNodeSizeMapping
Set Node Tooltip Bypass	setNodeTooltipBypass
Set Node Tooltip Default	setNodeTooltipDefault
Set Node Tooltip Mapping	setNodeTooltipMapping
Set Node Width Bypass	setNodeWidthBypass
Set Node Width Default	setNodeWidthDefault
Set Node Width Mapping	setNodeWidthMapping
setNotebookIsRunning	setNotebookIsRunning
setSandboxReinitialize	setSandboxReinitialize
Set Style Dependencies	setStyleDependencies
Set Visual Property Default	setVisualPropertyDefault
Set Visual Style	setVisualStyle
spoofResponse	spoofResponse spoofResponse-class
Sync Node Custom Graphics Size	syncNodeCustomGraphicsSize
Toggle Graphics Details	toggleGraphicsDetails
Ungroup Annotation Group	ungroupAnnotation
Unhide All	unhideAll
Unhide Edges	unhideEdges
Unhide Nodes	unhideNodes
Uninstall App	uninstallApp
Update Bounded Text Annotation	UpdateAnnotationBoundedText
Update Image Annotation	updateAnnotationImage
Update Shape Annotation	updateAnnotationShape
Update Text Annotation	updateAnnotationText
Update App	updateApp
Update Group Annotation	updateGroupAnnotation
Update Network In NDEx	updateNetworkInNDEx
Updates the default values of visual properties in a style	updateStyleDefaults
Updates a visual property mapping in a style	updateStyleMapping

Package: RCy3 2.27.0

RCy3: Functions to Access and Control Cytoscape

Overview of RCy3

Cytoscape and igraph

Cytoscape and graphNEL

Importing data

Network functions and visualization

Cancer networks and data

Identifier mapping

Upgrading existing scripts

Cytoscape and NDEx

Group nodes

Custom Graphics and Labels

Filtering Networks

Phylogenetic-trees

Jupyter Bridge and RCy3

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)