RCy3: Display and manipulate graphs in Cytoscape >= 3.3.0
Version 1.6.0

Vizualize, analyze and explore graphs, connecting R to Cytoscape (>= 3.3.0).

Browse man pages Browse package API and functions Browse package files

AuthorTanja Muetze, Georgi Kolishovski, Paul Shannon
Bioconductor views GraphAndNetwork Network ThirdPartyClient Visualization
Date of publicationNone
MaintainerTanja Muetze <tanja.muetze14@alumni.imperial.ac.uk>, Georgi Kolishovski <g_kolishv@yahoo.com>, Paul Shannon <pshannon@systemsbiology.org>
LicenseArtistic-2.0
Version1.6.0
URL https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RCy3")

Man pages

addCyEdge: addCyEdge
addCyNode: addCyNode
addGraphToGraph: addGraphToGraph
clearSelection: clearSelection
copyVisualStyle: copyVisualStyle
createWindow: createWindow
createWindowFromSelection: createWindowFromSelection
cy2.edge.names: cy2.edge.names
cyPlot: cyPlot
CytoscapeConnection: CytoscapeConnection
CytoscapeConnectionClass-class: Class "CytoscapeConnectionClass"
CytoscapeWindow: CytoscapeWindow
CytoscapeWindowClass-class: Class "CytoscapeWindowClass"
deleteAllWindows: deleteAllWindows
deleteEdgeAttribute: deleteEdgeAttribute
deleteNodeAttribute: deleteNodeAttribute
deleteSelectedEdges: deleteSelectedEdges
deleteSelectedNodes: deleteSelectedNodes
deleteWindow: deleteWindow
demoSimpleGraph: demoSimpleGraph
displayGraph: displayGraph
dockPanel: dockPanel
eda: eda
eda.names: eda.names
existing.CytoscapeWindow: existing.CytoscapeWindow
fitContent: fitContent
fitSelectedContent: fitSelectedContent
floatPanel: floatPanel
getAdjacentEdgeNames: getAdjacentEdgeNames
getAllEdgeAttributes: getAllEdgeAttributes
getAllEdges: getAllEdges
getAllNodeAttributes: getAllNodeAttributes
getAllNodes: getAllNodes
getArrowShapes: getArrowShapes
getAttributeClassNames: getAttributeClassNames
getCenter: getCenter
getDefaultBackgroundColor: getDefaultBackgroundColor
getDefaultEdgeReverseSelectionColor: getDefaultEdgeReverseSelectionColor
getDefaultEdgeSelectionColor: getDefaultEdgeSelectionColor
getDefaultNodeReverseSelectionColor: getDefaultNodeReverseSelectionColor
getDefaultNodeSelectionColor: getDefaultNodeSelectionColor
getDirectlyModifiableVisualProperties: getDirectlyModifiableVisualProperties
getEdgeAttribute: getEdgeAttribute
getEdgeAttributeNames: getEdgeAttributeNames
getEdgeCount: getEdgeCount
getFirstNeighbors: getFirstNeighbors
getGraph: getGraph
getGraphFromCyWindow: getGraphFromCyWindow
getLayoutNameMapping: getLayoutNameMapping
getLayoutNames: getLayoutNames
getLayoutPropertyNames: getLayoutPropertyNames
getLayoutPropertyType: getLayoutPropertyType
getLayoutPropertyValue: getLayoutPropertyValue
getLineStyles: getLineStyles
getNodeAttribute: getNodeAttribute
getNodeAttributeNames: getNodeAttributeNames
getNodeCount: getNodeCount
getNodePosition: getNodePosition
getNodeShapes: getNodeShapes
getNodeSize: getNodeSize
getSelectedEdgeCount: getSelectedEdgeCount
getSelectedEdges: getSelectedEdges
getSelectedNodeCount: getSelectedNodeCount
getSelectedNodes: getSelectedNodes
getViewCoordinates: getViewCoordinates
getVisualStyleNames: getVisualStyleNames
getWindowCount: getWindowCount
getWindowID: getWindowID
getWindowList: getWindowList
getZoom: getZoom
hideAllPanels: hideAllPanels
hideNodes: hideNodes
hidePanel: hidePanel
hideSelectedEdges: hideSelectedEdges
hideSelectedNodes: hideSelectedNodes
initEdgeAttribute: initEdgeAttribute
initNodeAttribute: initNodeAttribute
invertEdgeSelection: invertEdgeSelection
invertNodeSelection: invertNodeSelection
layoutNetwork: layoutNetwork
lockNodeDimensions: lockNodeDimensions
makeRandomGraph: makeRandomGraph
makeSimpleGraph: makeSimpleGraph
noa: noa
noa.names: noa.names
ping: ping
pluginVersion: pluginVersion
predictTimeToDisplayGraph: predictTimeToDisplayGraph
raiseWindow: raiseWindow
redraw: redraw
restoreLayout: restoreLayout
saveImage: saveImage
saveLayout: saveLayout
saveNetwork: saveNetwork
selectEdges: selectEdges
selectFirstNeighborsOfSelectedNodes: selectFirstNeighborsOfSelectedNodes
selectNodes: selectNodes
sendEdges: sendEdges
sendNodes: sendNodes
setCenter: setCenter
setDefaultBackgroundColor: setDefaultBackgroundColor
setDefaultEdgeColor: setDefaultEdgeColor
setDefaultEdgeFontSize: setDefaultEdgeFontSize
setDefaultEdgeLineWidth: setDefaultEdgeLineWidth
setDefaultEdgeReverseSelectionColor: setDefaultEdgeReverseSelectionColor
setDefaultEdgeSelectionColor: setDefaultEdgeSelectionColor
setDefaultEdgeSourceArrowColor: setDefaultEdgeSourceArrowColor
setDefaultEdgeTargetArrowColor: setDefaultEdgeTargetArrowColor
setDefaultNodeBorderColor: setDefaultNodeBorderColor
setDefaultNodeBorderWidth: setDefaultNodeBorderWidth
setDefaultNodeColor: setDefaultNodeColor
setDefaultNodeFontSize: setDefaultNodeFontSize
setDefaultNodeLabelColor: setDefaultNodeLabelColor
setDefaultNodeReverseSelectionColor: setDefaultNodeReverseSelectionColor
setDefaultNodeSelectionColor: setDefaultNodeSelectionColor
setDefaultNodeShape: setDefaultNodeShape
setDefaultNodeSize: setDefaultNodeSize
setEdgeAttributes: setEdgeAttributes
setEdgeAttributesDirect: setEdgeAttributesDirect
setEdgeColorDirect: setEdgeColorDirect
setEdgeColorRule: setEdgeColorRule
setEdgeFontSizeDirect: setEdgeFontSizeDirect
setEdgeLabelColorDirect: setEdgeLabelColorDirect
setEdgeLabelDirect: setEdgeLabelDirect
setEdgeLabelOpacityDirect: setEdgeLabelOpacityDirect
setEdgeLabelRule: setEdgeLabelRule
setEdgeLineStyleDirect: setEdgeLineStyleDirect
setEdgeLineStyleRule: specify the line styles to be used in drawing edges
setEdgeLineWidthDirect: setEdgeLineWidthDirect
setEdgeLineWidthRule: setEdgeLineWidthRule
setEdgeOpacityDirect: setEdgeOpacityDirect
setEdgeOpacityRule: setEdgeOpacityRule
setEdgeSourceArrowColorDirect: setEdgeSourceArrowColorDirect
setEdgeSourceArrowColorRule: Specify Rule for the Source Arrow Color
setEdgeSourceArrowOpacityDirect: setEdgeSourceArrowOpacityDirect
setEdgeSourceArrowRule: specify the arrow types to be used at the end of an edge at...
setEdgeSourceArrowShapeDirect: setEdgeSourceArrowShapeDirect
setEdgeTargetArrowColorDirect: setEdgeTargetArrowColorDirect
setEdgeTargetArrowColorRule: Specify rule for the target arrow color
setEdgeTargetArrowOpacityDirect: setEdgeTargetArrowOpacityDirect
setEdgeTargetArrowRule: specify the arrow types to be used at the end of an edge, at...
setEdgeTargetArrowShapeDirect: setEdgeTargetArrowShapeDirect
setEdgeTooltipDirect: setEdgeTooltipDirect
setEdgeTooltipRule: setEdgeTooltipRule
setGraph: setGraph
setLayoutProperties: setLayoutProperties
setNodeAttributes: setNodeAttributes
setNodeAttributesDirect: setNodeAttributesDirect
setNodeBorderColorDirect: setNodeBorderColorDirect
setNodeBorderColorRule: setNodeBorderColorRule
setNodeBorderOpacityDirect: setNodeBorderOpacityDirect
setNodeBorderWidthDirect: setNodeBorderWidthDirect
setNodeBorderWidthRule: setNodeBorderWidthRule
setNodeColorDirect: setNodeColorDirect
setNodeColorRule: setNodeColorRule
setNodeFillOpacityDirect: setNodeFillOpacityDirect
setNodeFontSizeDirect: setNodeFontSizeDirect
setNodeHeightDirect: setNodeHeightDirect
setNodeImageDirect: setNodeImageDirect
setNodeLabelColorDirect: setNodeLabelColorDirect
setNodeLabelDirect: setNodeLabelDirect
setNodeLabelOpacityDirect: setNodeLabelOpacityDirect
setNodeLabelRule: setNodeLabelRule
setNodeOpacityDirect: setNodeOpacityDirect
setNodeOpacityRule: setNodeOpacityRule
setNodePosition: setNodePosition
setNodeShapeDirect: setNodeShapeDirect
setNodeShapeRule: setNodeShapeRule
setNodeSizeDirect: setNodeSizeDirect
setNodeSizeRule: setNodeSizeRule
setNodeTooltipRule: setNodeTooltipRule
setNodeWidthDirect: setNodeWidthDirect
setTooltipDismissDelay: setTooltipDismissDelay
setTooltipInitialDelay: setTooltipInitialDelay
setVisualStyle: setVisualStyle
setWindowSize: setWindowSize
setZoom: setZoom
showGraphicsDetails: showGraphicsDetails
unhideAll: unhideAll

Functions

BBSOverride Source code
CytoscapeConnection Man page Source code
CytoscapeConnectionClass-class Man page
CytoscapeWindow Man page Source code
CytoscapeWindowClass-class Man page
addCyEdge Man page
addCyEdge,CytoscapeWindowClass-method Man page
addCyNode Man page
addCyNode,CytoscapeWindowClass-method Man page
addGraphToGraph Man page
addGraphToGraph,CytoscapeWindowClass-method Man page
check.cytoscape.plugin.version Source code
classicGraphToNodePairTable Source code
clearSelection Man page
clearSelection,CytoscapeWindowClass-method Man page
continuousMapping Source code
copyVisualStyle Man page
copyVisualStyle,CytoscapeConnectionClass-method Man page
createWindow Man page
createWindow,CytoscapeWindowClass-method Man page
createWindowFromSelection Man page
createWindowFromSelection,CytoscapeWindowClass-method Man page
cy2.edge.names Man page Source code
cyPlot Man page Source code
deleteAllWindows Man page
deleteAllWindows,CytoscapeConnectionClass-method Man page
deleteEdgeAttribute Man page
deleteEdgeAttribute,CytoscapeConnectionClass-method Man page
deleteNodeAttribute Man page
deleteNodeAttribute,CytoscapeConnectionClass-method Man page
deleteSelectedEdges Man page
deleteSelectedEdges,CytoscapeWindowClass-method Man page
deleteSelectedNodes Man page
deleteSelectedNodes,CytoscapeWindowClass-method Man page
deleteWindow Man page
deleteWindow,CytoscapeConnectionClass-method Man page
demoSimpleGraph Man page Source code
discreteMapping Source code
displayGraph Man page
displayGraph,CytoscapeWindowClass-method Man page
dockPanel Man page
dockPanel,CytoscapeConnectionClass-method Man page
eda Man page Source code
eda.names Man page Source code
existing.CytoscapeWindow Man page Source code
findColumnType Source code
fitContent Man page
fitContent,CytoscapeWindowClass-method Man page
fitSelectedContent Man page
fitSelectedContent,CytoscapeWindowClass-method Man page
floatPanel Man page
floatPanel,CytoscapeConnectionClass-method Man page
getAdjacentEdgeNames Man page Source code
getAllEdgeAttributes Man page
getAllEdgeAttributes,CytoscapeWindowClass-method Man page
getAllEdges Man page
getAllEdges,CytoscapeWindowClass-method Man page
getAllNodeAttributes Man page
getAllNodeAttributes,CytoscapeWindowClass-method Man page
getAllNodes Man page
getAllNodes,CytoscapeWindowClass-method Man page
getArrowShapes Man page
getArrowShapes,CytoscapeConnectionClass-method Man page
getAttributeClassNames Man page
getAttributeClassNames,CytoscapeConnectionClass-method Man page
getCenter Man page
getCenter,CytoscapeWindowClass-method Man page
getDefaultBackgroundColor Man page
getDefaultBackgroundColor,CytoscapeConnectionClass-method Man page
getDefaultEdgeReverseSelectionColor Man page
getDefaultEdgeReverseSelectionColor,CytoscapeConnectionClass-met Man page
getDefaultEdgeSelectionColor Man page
getDefaultEdgeSelectionColor,CytoscapeConnectionClass-method Man page
getDefaultNodeReverseSelectionColor Man page
getDefaultNodeReverseSelectionColor,CytoscapeConnectionClass-met Man page
getDefaultNodeSelectionColor Man page
getDefaultNodeSelectionColor,CytoscapeConnectionClass-method Man page
getDirectlyModifiableVisualProperties Man page
getDirectlyModifiableVisualProperties,CytoscapeConnectionClass-m Man page
getEdgeAttribute Man page
getEdgeAttribute,CytoscapeConnectionClass-method Man page
getEdgeAttributeNames Man page
getEdgeAttributeNames,CytoscapeConnectionClass-method Man page
getEdgeCount Man page
getEdgeCount,CytoscapeWindowClass-method Man page
getEdgeNamesAndSUIDS Source code
getFirstNeighbors Man page
getFirstNeighbors,CytoscapeWindowClass-method Man page
getGraph Man page
getGraph,CytoscapeWindowClass-method Man page
getGraphFromCyWindow Man page
getGraphFromCyWindow,CytoscapeConnectionClass-method Man page
getLayoutNameMapping Man page
getLayoutNameMapping,CytoscapeConnectionClass-method Man page
getLayoutNames Man page
getLayoutNames,CytoscapeConnectionClass-method Man page
getLayoutPropertyNames Man page
getLayoutPropertyNames,CytoscapeConnectionClass-method Man page
getLayoutPropertyType Man page
getLayoutPropertyType,CytoscapeConnectionClass-method Man page
getLayoutPropertyValue Man page
getLayoutPropertyValue,CytoscapeConnectionClass-method Man page
getLineStyles Man page
getLineStyles,CytoscapeConnectionClass-method Man page
getNodeAttribute Man page
getNodeAttribute,CytoscapeConnectionClass-method Man page
getNodeAttributeNames Man page
getNodeAttributeNames,CytoscapeConnectionClass-method Man page
getNodeCount Man page
getNodeCount,CytoscapeWindowClass-method Man page
getNodePosition Man page
getNodePosition,CytoscapeWindowClass-method Man page
getNodeShapes Man page
getNodeShapes,CytoscapeConnectionClass-method Man page
getNodeSize Man page
getNodeSize,CytoscapeWindowClass-method Man page
getNovelEdges Source code
getSelectedEdgeCount Man page
getSelectedEdgeCount,CytoscapeWindowClass-method Man page
getSelectedEdges Man page
getSelectedEdges,CytoscapeWindowClass-method Man page
getSelectedNodeCount Man page
getSelectedNodeCount,CytoscapeWindowClass-method Man page
getSelectedNodes Man page
getSelectedNodes,CytoscapeWindowClass-method Man page
getViewCoordinates Man page
getViewCoordinates,CytoscapeWindowClass-method Man page
getVisualProperty Source code
getVisualStyleNames Man page
getVisualStyleNames,CytoscapeConnectionClass-method Man page
getWindowCount Man page
getWindowCount,CytoscapeConnectionClass-method Man page
getWindowID Man page
getWindowID,CytoscapeConnectionClass-method Man page
getWindowList Man page
getWindowList,CytoscapeConnectionClass-method Man page
getZoom Man page
getZoom,CytoscapeWindowClass-method Man page
hideAllPanels Man page
hideAllPanels,CytoscapeConnectionClass-method Man page
hideNodes Man page
hideNodes,CytoscapeWindowClass-method Man page
hidePanel Man page
hidePanel,CytoscapeConnectionClass-method Man page
hideSelectedEdges Man page
hideSelectedEdges,CytoscapeWindowClass-method Man page
hideSelectedNodes Man page
hideSelectedNodes,CytoscapeWindowClass-method Man page
initEdgeAttribute Man page Source code
initNodeAttribute Man page Source code
invertEdgeSelection Man page
invertEdgeSelection,CytoscapeWindowClass-method Man page
invertNodeSelection Man page
invertNodeSelection,CytoscapeWindowClass-method Man page
is.classic.graph Source code
is.multiGraph Source code
layoutNetwork Man page
layoutNetwork,CytoscapeWindowClass-method Man page
lockNodeDimensions Man page
lockNodeDimensions,CytoscapeConnectionClass-method Man page
makeRandomGraph Man page Source code
makeSimpleGraph Man page Source code
multiGraphToNodePairTable Source code
noa Man page Source code
noa.names Man page Source code
obtainEveryOtherValue Source code
ping Man page
ping,CytoscapeConnectionClass-method Man page
pluginVersion Man page
pluginVersion,CytoscapeConnectionClass-method Man page
predictTimeToDisplayGraph Man page
predictTimeToDisplayGraph,CytoscapeWindowClass-method Man page
printf Source code
properlyInitializedEdgeAttribute Source code
properlyInitializedNodeAttribute Source code
raiseWindow Man page
raiseWindow,CytoscapeConnectionClass-method Man page
rcyEdgeNames Source code
redraw Man page
redraw,CytoscapeWindowClass-method Man page
remove.redundancies.in.undirected.graph Source code
remove.redundancies.in.undirected.graph.old Source code
restoreLayout Man page
restoreLayout,CytoscapeWindowClass-method Man page
sNotHexColor Source code
saveImage Man page
saveImage,CytoscapeWindowClass-method Man page
saveLayout Man page
saveLayout,CytoscapeWindowClass-method Man page
saveNetwork Man page
saveNetwork,CytoscapeWindowClass-method Man page
selectEdges Man page
selectEdges,CytoscapeWindowClass-method Man page
selectEdgesConnectedBySelectedNodes Source code
selectFirstNeighborsOfSelectedNodes Man page
selectFirstNeighborsOfSelectedNodes,CytoscapeWindowClass-method Man page
selectNodes Man page
selectNodes,CytoscapeWindowClass-method Man page
sendEdgeAttributesForGraph Source code
sendEdges Man page
sendEdges,CytoscapeWindowClass-method Man page
sendNodeAttributesForGraph Source code
sendNodes Man page
sendNodes,CytoscapeWindowClass-method Man page
setCenter Man page
setCenter,CytoscapeWindowClass-method Man page
setDefaultBackgroundColor Man page
setDefaultBackgroundColor,CytoscapeConnectionClass-method Man page
setDefaultEdgeColor Man page
setDefaultEdgeColor,CytoscapeConnectionClass-method Man page
setDefaultEdgeFontSize Man page
setDefaultEdgeFontSize,CytoscapeConnectionClass-method Man page
setDefaultEdgeLineWidth Man page
setDefaultEdgeLineWidth,CytoscapeConnectionClass-method Man page
setDefaultEdgeReverseSelectionColor Man page
setDefaultEdgeReverseSelectionColor,CytoscapeConnectionClass-met Man page
setDefaultEdgeSelectionColor Man page
setDefaultEdgeSelectionColor,CytoscapeConnectionClass-method Man page
setDefaultEdgeSourceArrowColor Man page
setDefaultEdgeSourceArrowColor,CytoscapeConnectionClass-method Man page
setDefaultEdgeTargetArrowColor Man page
setDefaultEdgeTargetArrowColor,CytoscapeConnectionClass-method Man page
setDefaultNodeBorderColor Man page
setDefaultNodeBorderColor,CytoscapeConnectionClass-method Man page
setDefaultNodeBorderWidth Man page
setDefaultNodeBorderWidth,CytoscapeConnectionClass-method Man page
setDefaultNodeColor Man page
setDefaultNodeColor,CytoscapeConnectionClass-method Man page
setDefaultNodeFontSize Man page
setDefaultNodeFontSize,CytoscapeConnectionClass-method Man page
setDefaultNodeLabelColor Man page
setDefaultNodeLabelColor,CytoscapeConnectionClass-method Man page
setDefaultNodeReverseSelectionColor Man page
setDefaultNodeReverseSelectionColor,CytoscapeConnectionClass-met Man page
setDefaultNodeSelectionColor Man page
setDefaultNodeSelectionColor,CytoscapeConnectionClass-method Man page
setDefaultNodeShape Man page
setDefaultNodeShape,CytoscapeConnectionClass-method Man page
setDefaultNodeSize Man page
setDefaultNodeSize,CytoscapeConnectionClass-method Man page
setEdgeAttributes Man page
setEdgeAttributes,CytoscapeWindowClass-method Man page
setEdgeAttributesDirect Man page
setEdgeAttributesDirect,CytoscapeWindowClass-method Man page
setEdgeColorDirect Man page
setEdgeColorDirect,CytoscapeWindowClass-method Man page
setEdgeColorRule Man page
setEdgeColorRule,CytoscapeWindowClass-method Man page
setEdgeFontSizeDirect Man page
setEdgeFontSizeDirect,CytoscapeWindowClass-method Man page
setEdgeLabelColorDirect Man page
setEdgeLabelColorDirect,CytoscapeWindowClass-method Man page
setEdgeLabelDirect Man page
setEdgeLabelDirect,CytoscapeWindowClass-method Man page
setEdgeLabelOpacityDirect Man page
setEdgeLabelOpacityDirect,CytoscapeWindowClass-method Man page
setEdgeLabelRule Man page
setEdgeLabelRule,CytoscapeWindowClass-method Man page
setEdgeLineStyleDirect Man page
setEdgeLineStyleDirect,CytoscapeWindowClass-method Man page
setEdgeLineStyleRule Man page
setEdgeLineStyleRule,CytoscapeWindowClass-method Man page
setEdgeLineWidthDirect Man page
setEdgeLineWidthDirect,CytoscapeWindowClass-method Man page
setEdgeLineWidthRule Man page
setEdgeLineWidthRule,CytoscapeWindowClass-method Man page
setEdgeOpacityDirect Man page
setEdgeOpacityDirect,CytoscapeWindowClass-method Man page
setEdgeOpacityRule Man page
setEdgeOpacityRule,CytoscapeWindowClass-method Man page
setEdgePropertyDirect Source code
setEdgeSourceArrowColorDirect Man page
setEdgeSourceArrowColorDirect,CytoscapeWindowClass-method Man page
setEdgeSourceArrowColorRule Man page
setEdgeSourceArrowColorRule,CytoscapeWindowClass-method Man page
setEdgeSourceArrowOpacityDirect Man page
setEdgeSourceArrowOpacityDirect,CytoscapeWindowClass-method Man page
setEdgeSourceArrowRule Man page
setEdgeSourceArrowRule,CytoscapeWindowClass-method Man page
setEdgeSourceArrowShapeDirect Man page
setEdgeSourceArrowShapeDirect,CytoscapeWindowClass-method Man page
setEdgeTargetArrowColorDirect Man page
setEdgeTargetArrowColorDirect,CytoscapeWindowClass-method Man page
setEdgeTargetArrowColorRule Man page
setEdgeTargetArrowColorRule,CytoscapeWindowClass-method Man page
setEdgeTargetArrowOpacityDirect Man page
setEdgeTargetArrowOpacityDirect,CytoscapeWindowClass-method Man page
setEdgeTargetArrowRule Man page
setEdgeTargetArrowRule,CytoscapeWindowClass-method Man page
setEdgeTargetArrowShapeDirect Man page
setEdgeTargetArrowShapeDirect,CytoscapeWindowClass-method Man page
setEdgeTooltipDirect Man page
setEdgeTooltipDirect,CytoscapeWindowClass-method Man page
setEdgeTooltipRule Man page
setEdgeTooltipRule,CytoscapeWindowClass-method Man page
setGraph Man page
setGraph,CytoscapeWindowClass-method Man page
setLayoutProperties Man page
setLayoutProperties,CytoscapeConnectionClass-method Man page
setNodeAttributes Man page
setNodeAttributes,CytoscapeWindowClass-method Man page
setNodeAttributesDirect Man page
setNodeAttributesDirect,CytoscapeWindowClass-method Man page
setNodeBorderColorDirect Man page
setNodeBorderColorDirect,CytoscapeWindowClass-method Man page
setNodeBorderColorRule Man page
setNodeBorderColorRule,CytoscapeWindowClass-method Man page
setNodeBorderOpacityDirect Man page
setNodeBorderOpacityDirect,CytoscapeWindowClass-method Man page
setNodeBorderWidthDirect Man page
setNodeBorderWidthDirect,CytoscapeWindowClass-method Man page
setNodeBorderWidthRule Man page
setNodeBorderWidthRule,CytoscapeWindowClass-method Man page
setNodeColorDirect Man page
setNodeColorDirect,CytoscapeWindowClass-method Man page
setNodeColorRule Man page
setNodeColorRule,CytoscapeWindowClass-method Man page
setNodeFillOpacityDirect Man page
setNodeFillOpacityDirect,CytoscapeWindowClass-method Man page
setNodeFontSizeDirect Man page
setNodeFontSizeDirect,CytoscapeWindowClass-method Man page
setNodeHeightDirect Man page
setNodeHeightDirect,CytoscapeWindowClass-method Man page
setNodeImageDirect Man page
setNodeImageDirect,CytoscapeWindowClass-method Man page
setNodeLabelColorDirect Man page
setNodeLabelColorDirect,CytoscapeWindowClass-method Man page
setNodeLabelDirect Man page
setNodeLabelDirect,CytoscapeWindowClass-method Man page
setNodeLabelOpacityDirect Man page
setNodeLabelOpacityDirect,CytoscapeWindowClass-method Man page
setNodeLabelRule Man page
setNodeLabelRule,CytoscapeWindowClass-method Man page
setNodeOpacityDirect Man page
setNodeOpacityDirect,CytoscapeWindowClass-method Man page
setNodeOpacityRule Man page
setNodeOpacityRule,CytoscapeWindowClass-method Man page
setNodePosition Man page
setNodePosition,CytoscapeWindowClass-method Man page
setNodePropertyDirect Source code
setNodeShapeDirect Man page
setNodeShapeDirect,CytoscapeWindowClass-method Man page
setNodeShapeRule Man page
setNodeShapeRule,CytoscapeWindowClass-method Man page
setNodeSizeDirect Man page
setNodeSizeDirect,CytoscapeWindowClass-method Man page
setNodeSizeRule Man page
setNodeSizeRule,CytoscapeWindowClass-method Man page
setNodeTooltipRule Man page
setNodeTooltipRule,CytoscapeWindowClass-method Man page
setNodeWidthDirect Man page
setNodeWidthDirect,CytoscapeWindowClass-method Man page
setTooltipDismissDelay Man page
setTooltipDismissDelay,CytoscapeConnectionClass-method Man page
setTooltipInitialDelay Man page
setTooltipInitialDelay,CytoscapeConnectionClass-method Man page
setVisualProperty Source code
setVisualStyle Man page
setVisualStyle,CytoscapeConnectionClass-method Man page
setWindowSize Man page
setWindowSize,CytoscapeWindowClass-method Man page
setZoom Man page
setZoom,CytoscapeWindowClass-method Man page
sfn Man page
sfn,CytoscapeWindowClass-method Man page
showGraphicsDetails Man page
showGraphicsDetails,CytoscapeConnectionClass-method Man page
simpleCap Source code
unhideAll Man page
unhideAll,CytoscapeWindowClass-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RCy3.R
README
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/RCy3.R
inst/doc/RCy3.Rnw
inst/doc/RCy3.pdf
inst/unitTests
inst/unitTests/test_RCy3.R
man
man/CytoscapeConnection.Rd
man/CytoscapeConnectionClass-class.Rd
man/CytoscapeWindow.Rd
man/CytoscapeWindowClass-class.Rd
man/addCyEdge.Rd
man/addCyNode.Rd
man/addGraphToGraph.Rd
man/clearSelection.Rd
man/copyVisualStyle.Rd
man/createWindow.Rd
man/createWindowFromSelection.Rd
man/cy2.edge.names.Rd
man/cyPlot.Rd
man/deleteAllWindows.Rd
man/deleteEdgeAttribute.Rd
man/deleteNodeAttribute.Rd
man/deleteSelectedEdges.Rd
man/deleteSelectedNodes.Rd
man/deleteWindow.Rd
man/demoSimpleGraph.Rd
man/displayGraph.Rd
man/dockPanel.Rd
man/eda.Rd
man/eda.names.Rd
man/existing.CytoscapeWindow.Rd
man/fitContent.Rd
man/fitSelectedContent.Rd
man/floatPanel.Rd
man/getAdjacentEdgeNames.Rd
man/getAllEdgeAttributes.Rd
man/getAllEdges.Rd
man/getAllNodeAttributes.Rd
man/getAllNodes.Rd
man/getArrowShapes.Rd
man/getAttributeClassNames.Rd
man/getCenter.Rd
man/getDefaultBackgroundColor.Rd
man/getDefaultEdgeReverseSelectionColor.Rd
man/getDefaultEdgeSelectionColor.Rd
man/getDefaultNodeReverseSelectionColor.Rd
man/getDefaultNodeSelectionColor.Rd
man/getDirectlyModifiableVisualProperties.Rd
man/getEdgeAttribute.Rd
man/getEdgeAttributeNames.Rd
man/getEdgeCount.Rd
man/getFirstNeighbors.Rd
man/getGraph.Rd
man/getGraphFromCyWindow.Rd
man/getLayoutNameMapping.Rd
man/getLayoutNames.Rd
man/getLayoutPropertyNames.Rd
man/getLayoutPropertyType.Rd
man/getLayoutPropertyValue.Rd
man/getLineStyles.Rd
man/getNodeAttribute.Rd
man/getNodeAttributeNames.Rd
man/getNodeCount.Rd
man/getNodePosition.Rd
man/getNodeShapes.Rd
man/getNodeSize.Rd
man/getSelectedEdgeCount.Rd
man/getSelectedEdges.Rd
man/getSelectedNodeCount.Rd
man/getSelectedNodes.Rd
man/getViewCoordinates.Rd
man/getVisualStyleNames.Rd
man/getWindowCount.Rd
man/getWindowID.Rd
man/getWindowList.Rd
man/getZoom.Rd
man/hideAllPanels.Rd
man/hideNodes.Rd
man/hidePanel.Rd
man/hideSelectedEdges.Rd
man/hideSelectedNodes.Rd
man/initEdgeAttribute.Rd
man/initNodeAttribute.Rd
man/invertEdgeSelection.Rd
man/invertNodeSelection.Rd
man/layoutNetwork.Rd
man/lockNodeDimensions.Rd
man/makeRandomGraph.Rd
man/makeSimpleGraph.Rd
man/noa.Rd
man/noa.names.Rd
man/ping.Rd
man/pluginVersion.Rd
man/predictTimeToDisplayGraph.Rd
man/raiseWindow.Rd
man/redraw.Rd
man/restoreLayout.Rd
man/saveImage.Rd
man/saveLayout.Rd
man/saveNetwork.Rd
man/selectEdges.Rd
man/selectFirstNeighborsOfSelectedNodes.Rd
man/selectNodes.Rd
man/sendEdges.Rd
man/sendNodes.Rd
man/setCenter.Rd
man/setDefaultBackgroundColor.Rd
man/setDefaultEdgeColor.Rd
man/setDefaultEdgeFontSize.Rd
man/setDefaultEdgeLineWidth.Rd
man/setDefaultEdgeReverseSelectionColor.Rd
man/setDefaultEdgeSelectionColor.Rd
man/setDefaultEdgeSourceArrowColor.Rd
man/setDefaultEdgeTargetArrowColor.Rd
man/setDefaultNodeBorderColor.Rd
man/setDefaultNodeBorderWidth.Rd
man/setDefaultNodeColor.Rd
man/setDefaultNodeFontSize.Rd
man/setDefaultNodeLabelColor.Rd
man/setDefaultNodeReverseSelectionColor.Rd
man/setDefaultNodeSelectionColor.Rd
man/setDefaultNodeShape.Rd
man/setDefaultNodeSize.Rd
man/setEdgeAttributes.Rd
man/setEdgeAttributesDirect.Rd
man/setEdgeColorDirect.Rd
man/setEdgeColorRule.Rd
man/setEdgeFontSizeDirect.Rd
man/setEdgeLabelColorDirect.Rd
man/setEdgeLabelDirect.Rd
man/setEdgeLabelOpacityDirect.Rd
man/setEdgeLabelRule.Rd
man/setEdgeLineStyleDirect.Rd
man/setEdgeLineStyleRule.Rd
man/setEdgeLineWidthDirect.Rd
man/setEdgeLineWidthRule.Rd
man/setEdgeOpacityDirect.Rd
man/setEdgeOpacityRule.Rd
man/setEdgeSourceArrowColorDirect.Rd
man/setEdgeSourceArrowColorRule.Rd
man/setEdgeSourceArrowOpacityDirect.Rd
man/setEdgeSourceArrowRule.Rd
man/setEdgeSourceArrowShapeDirect.Rd
man/setEdgeTargetArrowColorDirect.Rd
man/setEdgeTargetArrowColorRule.Rd
man/setEdgeTargetArrowOpacityDirect.Rd
man/setEdgeTargetArrowRule.Rd
man/setEdgeTargetArrowShapeDirect.Rd
man/setEdgeTooltipDirect.Rd
man/setEdgeTooltipRule.Rd
man/setGraph.Rd
man/setLayoutProperties.Rd
man/setNodeAttributes.Rd
man/setNodeAttributesDirect.Rd
man/setNodeBorderColorDirect.Rd
man/setNodeBorderColorRule.Rd
man/setNodeBorderOpacityDirect.Rd
man/setNodeBorderWidthDirect.Rd
man/setNodeBorderWidthRule.Rd
man/setNodeColorDirect.Rd
man/setNodeColorRule.Rd
man/setNodeFillOpacityDirect.Rd
man/setNodeFontSizeDirect.Rd
man/setNodeHeightDirect.Rd
man/setNodeImageDirect.Rd
man/setNodeLabelColorDirect.Rd
man/setNodeLabelDirect.Rd
man/setNodeLabelOpacityDirect.Rd
man/setNodeLabelRule.Rd
man/setNodeOpacityDirect.Rd
man/setNodeOpacityRule.Rd
man/setNodePosition.Rd
man/setNodeShapeDirect.Rd
man/setNodeShapeRule.Rd
man/setNodeSizeDirect.Rd
man/setNodeSizeRule.Rd
man/setNodeTooltipRule.Rd
man/setNodeWidthDirect.Rd
man/setTooltipDismissDelay.Rd
man/setTooltipInitialDelay.Rd
man/setVisualStyle.Rd
man/setWindowSize.Rd
man/setZoom.Rd
man/showGraphicsDetails.Rd
man/unhideAll.Rd
tests
tests/runTests.R
vignettes
vignettes/RCy3.Rnw
RCy3 documentation built on May 20, 2017, 9:53 p.m.