RCy3: Display and manipulate graphs in Cytoscape >= 3.3.0

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RCy3")
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
Version1.5.2
https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape

View on Bioconductor

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

addCyEdge Man page
addCyEdge,CytoscapeWindowClass-method Man page
addCyNode Man page
addCyNode,CytoscapeWindowClass-method Man page
addGraphToGraph Man page
addGraphToGraph,CytoscapeWindowClass-method Man page
clearSelection Man page
clearSelection,CytoscapeWindowClass-method Man page
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
cyPlot Man page
CytoscapeConnection Man page
CytoscapeConnectionClass-class Man page
CytoscapeWindow Man page
CytoscapeWindowClass-class Man page
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
displayGraph Man page
displayGraph,CytoscapeWindowClass-method Man page
dockPanel Man page
dockPanel,CytoscapeConnectionClass-method Man page
eda Man page
eda.names Man page
existing.CytoscapeWindow Man page
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
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
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
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
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
initNodeAttribute Man page
invertEdgeSelection Man page
invertEdgeSelection,CytoscapeWindowClass-method Man page
invertNodeSelection Man page
invertNodeSelection,CytoscapeWindowClass-method Man page
layoutNetwork Man page
layoutNetwork,CytoscapeWindowClass-method Man page
lockNodeDimensions Man page
lockNodeDimensions,CytoscapeConnectionClass-method Man page
makeRandomGraph Man page
makeSimpleGraph Man page
noa Man page
noa.names Man page
ping Man page
ping,CytoscapeConnectionClass-method Man page
pluginVersion Man page
pluginVersion,CytoscapeConnectionClass-method Man page
predictTimeToDisplayGraph Man page
predictTimeToDisplayGraph,CytoscapeWindowClass-method Man page
raiseWindow Man page
raiseWindow,CytoscapeConnectionClass-method Man page
redraw Man page
redraw,CytoscapeWindowClass-method Man page
restoreLayout Man page
restoreLayout,CytoscapeWindowClass-method Man page
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
selectFirstNeighborsOfSelectedNodes Man page
selectFirstNeighborsOfSelectedNodes,CytoscapeWindowClass-method Man page
selectNodes Man page
selectNodes,CytoscapeWindowClass-method Man page
sendEdges Man page
sendEdges,CytoscapeWindowClass-method Man page
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
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
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
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
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

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