RCy3: Display and manipulate graphs in Cytoscape >= 3.3.0

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

AuthorTanja Muetze, Georgi Kolishovski, Paul Shannon
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

Files in this package

RCy3/DESCRIPTION
RCy3/NAMESPACE
RCy3/NEWS
RCy3/R
RCy3/R/RCy3.R
RCy3/README
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/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

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