RCytoscape: Display and manipulate graphs in Cytoscape

Interactvive viewing and exploration of graphs, connecting R to Cytoscape.

AuthorPaul Shannon
Date of publicationNone
MaintainerPaul Shannon <pshannon@systemsbiology.org>
LicenseGPL-2
Version1.24.1
http://rcytoscape.systemsbiology.net

View on Bioconductor

Man pages

addCyEdge: addCyEdge

addCyNode: addCyNode

addGraphToGraph: addGraphToGraph

clearMsg: clearMsg

clearSelection: clearSelection

copyVisualStyle: copyVisualStyle

createWindow: createWindow

createWindowFromSelection: createWindowFromSelection

cy2.edge.names: cy2.edge.names

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

msg: msg

new.CytoscapeWindow: new.CytoscapeWindow

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

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

setEdgeLabelWidthDirect: setEdgeLabelWidthDirect

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

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

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