RCy3: Display and manipulate graphs in Cytoscape >= 3.3.0

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

Author
Tanja Muetze, Georgi Kolishovski, Paul Shannon
Date of publication
None
Maintainer
Tanja Muetze <tanja.muetze14@imperial.ac.uk>, Georgi Kolishovski <g_kolishv@yahoo.com>, Paul Shannon <pshannon@systemsbiology.org>
License
Artistic-2.0
Version
1.2.0

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

Files in this package

RCy3/.BBSoptions
RCy3/DESCRIPTION
RCy3/NAMESPACE
RCy3/NEWS
RCy3/R
RCy3/R/RCy3.R
RCy3/README
RCy3/README.md
RCy3/build
RCy3/build/vignette.rds
RCy3/inst
RCy3/inst/CITATION
RCy3/inst/doc
RCy3/inst/doc/RCy3.R
RCy3/inst/doc/RCy3.Rnw
RCy3/inst/doc/RCy3.pdf
RCy3/inst/unitTests
RCy3/inst/unitTests/RCy3_unit_tests.R
RCy3/inst/unitTests/test_RCy3.R
RCy3/man
RCy3/man/CytoscapeConnection.Rd
RCy3/man/CytoscapeConnectionClass-class.Rd
RCy3/man/CytoscapeWindow.Rd
RCy3/man/CytoscapeWindowClass-class.Rd
RCy3/man/addCyEdge.Rd
RCy3/man/addCyNode.Rd
RCy3/man/addGraphToGraph.Rd
RCy3/man/clearSelection.Rd
RCy3/man/copyVisualStyle.Rd
RCy3/man/createWindow.Rd
RCy3/man/createWindowFromSelection.Rd
RCy3/man/cy2.edge.names.Rd
RCy3/man/cyPlot.Rd
RCy3/man/deleteAllWindows.Rd
RCy3/man/deleteEdgeAttribute.Rd
RCy3/man/deleteNodeAttribute.Rd
RCy3/man/deleteSelectedEdges.Rd
RCy3/man/deleteSelectedNodes.Rd
RCy3/man/deleteWindow.Rd
RCy3/man/demoSimpleGraph.Rd
RCy3/man/displayGraph.Rd
RCy3/man/dockPanel.Rd
RCy3/man/eda.Rd
RCy3/man/eda.names.Rd
RCy3/man/existing.CytoscapeWindow.Rd
RCy3/man/fitContent.Rd
RCy3/man/fitSelectedContent.Rd
RCy3/man/floatPanel.Rd
RCy3/man/getAdjacentEdgeNames.Rd
RCy3/man/getAllEdgeAttributes.Rd
RCy3/man/getAllEdges.Rd
RCy3/man/getAllNodeAttributes.Rd
RCy3/man/getAllNodes.Rd
RCy3/man/getArrowShapes.Rd
RCy3/man/getAttributeClassNames.Rd
RCy3/man/getCenter.Rd
RCy3/man/getDefaultBackgroundColor.Rd
RCy3/man/getDefaultEdgeReverseSelectionColor.Rd
RCy3/man/getDefaultEdgeSelectionColor.Rd
RCy3/man/getDefaultNodeReverseSelectionColor.Rd
RCy3/man/getDefaultNodeSelectionColor.Rd
RCy3/man/getDirectlyModifiableVisualProperties.Rd
RCy3/man/getEdgeAttribute.Rd
RCy3/man/getEdgeAttributeNames.Rd
RCy3/man/getEdgeCount.Rd
RCy3/man/getFirstNeighbors.Rd
RCy3/man/getGraph.Rd
RCy3/man/getGraphFromCyWindow.Rd
RCy3/man/getLayoutNameMapping.Rd
RCy3/man/getLayoutNames.Rd
RCy3/man/getLayoutPropertyNames.Rd
RCy3/man/getLayoutPropertyType.Rd
RCy3/man/getLayoutPropertyValue.Rd
RCy3/man/getLineStyles.Rd
RCy3/man/getNodeAttribute.Rd
RCy3/man/getNodeAttributeNames.Rd
RCy3/man/getNodeCount.Rd
RCy3/man/getNodePosition.Rd
RCy3/man/getNodeShapes.Rd
RCy3/man/getNodeSize.Rd
RCy3/man/getSelectedEdgeCount.Rd
RCy3/man/getSelectedEdges.Rd
RCy3/man/getSelectedNodeCount.Rd
RCy3/man/getSelectedNodes.Rd
RCy3/man/getViewCoordinates.Rd
RCy3/man/getVisualStyleNames.Rd
RCy3/man/getWindowCount.Rd
RCy3/man/getWindowID.Rd
RCy3/man/getWindowList.Rd
RCy3/man/getZoom.Rd
RCy3/man/hideAllPanels.Rd
RCy3/man/hideNodes.Rd
RCy3/man/hidePanel.Rd
RCy3/man/hideSelectedEdges.Rd
RCy3/man/hideSelectedNodes.Rd
RCy3/man/initEdgeAttribute.Rd
RCy3/man/initNodeAttribute.Rd
RCy3/man/invertEdgeSelection.Rd
RCy3/man/invertNodeSelection.Rd
RCy3/man/layoutNetwork.Rd
RCy3/man/lockNodeDimensions.Rd
RCy3/man/makeRandomGraph.Rd
RCy3/man/makeSimpleGraph.Rd
RCy3/man/noa.Rd
RCy3/man/noa.names.Rd
RCy3/man/ping.Rd
RCy3/man/pluginVersion.Rd
RCy3/man/predictTimeToDisplayGraph.Rd
RCy3/man/raiseWindow.Rd
RCy3/man/redraw.Rd
RCy3/man/restoreLayout.Rd
RCy3/man/saveImage.Rd
RCy3/man/saveLayout.Rd
RCy3/man/saveNetwork.Rd
RCy3/man/selectEdges.Rd
RCy3/man/selectFirstNeighborsOfSelectedNodes.Rd
RCy3/man/selectNodes.Rd
RCy3/man/sendEdges.Rd
RCy3/man/sendNodes.Rd
RCy3/man/setCenter.Rd
RCy3/man/setDefaultBackgroundColor.Rd
RCy3/man/setDefaultEdgeColor.Rd
RCy3/man/setDefaultEdgeFontSize.Rd
RCy3/man/setDefaultEdgeLineWidth.Rd
RCy3/man/setDefaultEdgeReverseSelectionColor.Rd
RCy3/man/setDefaultEdgeSelectionColor.Rd
RCy3/man/setDefaultEdgeSourceArrowColor.Rd
RCy3/man/setDefaultEdgeTargetArrowColor.Rd
RCy3/man/setDefaultNodeBorderColor.Rd
RCy3/man/setDefaultNodeBorderWidth.Rd
RCy3/man/setDefaultNodeColor.Rd
RCy3/man/setDefaultNodeFontSize.Rd
RCy3/man/setDefaultNodeLabelColor.Rd
RCy3/man/setDefaultNodeReverseSelectionColor.Rd
RCy3/man/setDefaultNodeSelectionColor.Rd
RCy3/man/setDefaultNodeShape.Rd
RCy3/man/setDefaultNodeSize.Rd
RCy3/man/setEdgeAttributes.Rd
RCy3/man/setEdgeAttributesDirect.Rd
RCy3/man/setEdgeColorDirect.Rd
RCy3/man/setEdgeColorRule.Rd
RCy3/man/setEdgeFontSizeDirect.Rd
RCy3/man/setEdgeLabelColorDirect.Rd
RCy3/man/setEdgeLabelDirect.Rd
RCy3/man/setEdgeLabelOpacityDirect.Rd
RCy3/man/setEdgeLabelRule.Rd
RCy3/man/setEdgeLineStyleDirect.Rd
RCy3/man/setEdgeLineStyleRule.Rd
RCy3/man/setEdgeLineWidthDirect.Rd
RCy3/man/setEdgeLineWidthRule.Rd
RCy3/man/setEdgeOpacityDirect.Rd
RCy3/man/setEdgeOpacityRule.Rd
RCy3/man/setEdgeSourceArrowColorDirect.Rd
RCy3/man/setEdgeSourceArrowColorRule.Rd
RCy3/man/setEdgeSourceArrowOpacityDirect.Rd
RCy3/man/setEdgeSourceArrowRule.Rd
RCy3/man/setEdgeSourceArrowShapeDirect.Rd
RCy3/man/setEdgeTargetArrowColorDirect.Rd
RCy3/man/setEdgeTargetArrowColorRule.Rd
RCy3/man/setEdgeTargetArrowOpacityDirect.Rd
RCy3/man/setEdgeTargetArrowRule.Rd
RCy3/man/setEdgeTargetArrowShapeDirect.Rd
RCy3/man/setEdgeTooltipDirect.Rd
RCy3/man/setEdgeTooltipRule.Rd
RCy3/man/setGraph.Rd
RCy3/man/setLayoutProperties.Rd
RCy3/man/setNodeAttributes.Rd
RCy3/man/setNodeAttributesDirect.Rd
RCy3/man/setNodeBorderColorDirect.Rd
RCy3/man/setNodeBorderColorRule.Rd
RCy3/man/setNodeBorderOpacityDirect.Rd
RCy3/man/setNodeBorderWidthDirect.Rd
RCy3/man/setNodeBorderWidthRule.Rd
RCy3/man/setNodeColorDirect.Rd
RCy3/man/setNodeColorRule.Rd
RCy3/man/setNodeFillOpacityDirect.Rd
RCy3/man/setNodeFontSizeDirect.Rd
RCy3/man/setNodeHeightDirect.Rd
RCy3/man/setNodeImageDirect.Rd
RCy3/man/setNodeLabelColorDirect.Rd
RCy3/man/setNodeLabelDirect.Rd
RCy3/man/setNodeLabelOpacityDirect.Rd
RCy3/man/setNodeLabelRule.Rd
RCy3/man/setNodeOpacityDirect.Rd
RCy3/man/setNodeOpacityRule.Rd
RCy3/man/setNodePosition.Rd
RCy3/man/setNodeShapeDirect.Rd
RCy3/man/setNodeShapeRule.Rd
RCy3/man/setNodeSizeDirect.Rd
RCy3/man/setNodeSizeRule.Rd
RCy3/man/setNodeTooltipRule.Rd
RCy3/man/setNodeWidthDirect.Rd
RCy3/man/setTooltipDismissDelay.Rd
RCy3/man/setTooltipInitialDelay.Rd
RCy3/man/setVisualStyle.Rd
RCy3/man/setWindowSize.Rd
RCy3/man/setZoom.Rd
RCy3/man/showGraphicsDetails.Rd
RCy3/man/unhideAll.Rd
RCy3/tests
RCy3/tests/runTests.R
RCy3/vignettes
RCy3/vignettes/RCy3.Rnw