# Display and manipulate graphs in Cytoscape

## Documentation for package ‘RCytoscape’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I L M N P R S U

## -- A --

addCyEdge | addCyEdge
addCyEdge-method | addCyEdge
addCyNode | addCyNode
addCyNode-method | addCyNode
addGraphToGraph | addGraphToGraph
addGraphToGraph-method | addGraphToGraph

## -- C --

clearMsg | clearMsg
clearMsg-method | clearMsg
clearSelection | clearSelection
clearSelection-method | clearSelection
copyVisualStyle | copyVisualStyle
copyVisualStyle-method | copyVisualStyle
createWindow | createWindow
createWindow-method | createWindow
createWindowFromSelection | createWindowFromSelection
createWindowFromSelection-method | createWindowFromSelection
cy2.edge.names | cy2.edge.names
CytoscapeConnection | CytoscapeConnection
CytoscapeConnectionClass-class | Class "CytoscapeConnectionClass"
CytoscapeWindow | CytoscapeWindow
CytoscapeWindowClass-class | Class "CytoscapeWindowClass"

## -- D --

deleteAllWindows | deleteAllWindows
deleteAllWindows-method | deleteAllWindows
deleteEdgeAttribute | deleteEdgeAttribute
deleteEdgeAttribute-method | deleteEdgeAttribute
deleteNodeAttribute | deleteNodeAttribute
deleteNodeAttribute-method | deleteNodeAttribute
deleteSelectedEdges | deleteSelectedEdges
deleteSelectedEdges-method | deleteSelectedEdges
deleteSelectedNodes | deleteSelectedNodes
deleteSelectedNodes-method | deleteSelectedNodes
deleteWindow | deleteWindow
deleteWindow-method | deleteWindow
demoSimpleGraph | demoSimpleGraph
displayGraph | displayGraph
displayGraph-method | displayGraph
dockPanel | dockPanel
dockPanel-method | dockPanel

## -- E --

eda | eda
eda.names | eda.names
existing.CytoscapeWindow | existing.CytoscapeWindow

## -- F --

fitContent | fitContent
fitContent-method | fitContent
fitSelectedContent | fitSelectedContent
fitSelectedContent-method | fitSelectedContent
floatPanel | floatPanel
floatPanel-method | floatPanel

## -- G --

getAdjacentEdgeNames | getAdjacentEdgeNames
getAllEdgeAttributes | getAllEdgeAttributes
getAllEdgeAttributes-method | getAllEdgeAttributes
getAllEdges | getAllEdges
getAllEdges-method | getAllEdges
getAllNodeAttributes | getAllNodeAttributes
getAllNodeAttributes-method | getAllNodeAttributes
getAllNodes | getAllNodes
getAllNodes-method | getAllNodes
getArrowShapes | getArrowShapes
getArrowShapes-method | getArrowShapes
getAttributeClassNames | getAttributeClassNames
getAttributeClassNames-method | getAttributeClassNames
getCenter | getCenter
getCenter-method | getCenter
getDefaultBackgroundColor | getDefaultBackgroundColor
getDefaultBackgroundColor-method | getDefaultBackgroundColor
getDefaultEdgeReverseSelectionColor | getDefaultEdgeReverseSelectionColor
getDefaultEdgeReverseSelectionColor-method | getDefaultEdgeReverseSelectionColor
getDefaultEdgeSelectionColor | getDefaultEdgeSelectionColor
getDefaultEdgeSelectionColor-method | getDefaultEdgeSelectionColor
getDefaultNodeReverseSelectionColor | getDefaultNodeReverseSelectionColor
getDefaultNodeReverseSelectionColor-method | getDefaultNodeReverseSelectionColor
getDefaultNodeSelectionColor | getDefaultNodeSelectionColor
getDefaultNodeSelectionColor-method | getDefaultNodeSelectionColor
getDirectlyModifiableVisualProperties | getDirectlyModifiableVisualProperties
getDirectlyModifiableVisualProperties-method | getDirectlyModifiableVisualProperties
getEdgeAttribute | getEdgeAttribute
getEdgeAttribute-method | getEdgeAttribute
getEdgeAttributeNames | getEdgeAttributeNames
getEdgeAttributeNames-method | getEdgeAttributeNames
getEdgeCount | getEdgeCount
getEdgeCount-method | getEdgeCount
getFirstNeighbors | getFirstNeighbors
getFirstNeighbors-method | getFirstNeighbors
getGraph | getGraph
getGraph-method | getGraph
getGraphFromCyWindow | getGraphFromCyWindow
getGraphFromCyWindow-method | getGraphFromCyWindow
getLayoutNameMapping | getLayoutNameMapping
getLayoutNameMapping-method | getLayoutNameMapping
getLayoutNames | getLayoutNames
getLayoutNames-method | getLayoutNames
getLayoutPropertyNames | getLayoutPropertyNames
getLayoutPropertyNames-method | getLayoutPropertyNames
getLayoutPropertyType | getLayoutPropertyType
getLayoutPropertyType-method | getLayoutPropertyType
getLayoutPropertyValue | getLayoutPropertyValue
getLayoutPropertyValue-method | getLayoutPropertyValue
getLineStyles | getLineStyles
getLineStyles-method | getLineStyles
getNodeAttribute | getNodeAttribute
getNodeAttribute-method | getNodeAttribute
getNodeAttributeNames | getNodeAttributeNames
getNodeAttributeNames-method | getNodeAttributeNames
getNodeCount | getNodeCount
getNodeCount-method | getNodeCount
getNodePosition | getNodePosition
getNodePosition-method | getNodePosition
getNodeShapes | getNodeShapes
getNodeShapes-method | getNodeShapes
getNodeSize | getNodeSize
getNodeSize-method | getNodeSize
getSelectedEdgeCount | getSelectedEdgeCount
getSelectedEdgeCount-method | getSelectedEdgeCount
getSelectedEdges | getSelectedEdges
getSelectedEdges-method | getSelectedEdges
getSelectedNodeCount | getSelectedNodeCount
getSelectedNodeCount-method | getSelectedNodeCount
getSelectedNodes | getSelectedNodes
getSelectedNodes-method | getSelectedNodes
getViewCoordinates | getViewCoordinates
getViewCoordinates-method | getViewCoordinates
getVisualStyleNames | getVisualStyleNames
getVisualStyleNames-method | getVisualStyleNames
getWindowCount | getWindowCount
getWindowCount-method | getWindowCount
getWindowID | getWindowID
getWindowID-method | getWindowID
getWindowList | getWindowList
getWindowList-method | getWindowList
getZoom | getZoom
getZoom-method | getZoom

## -- H --

hideAllPanels | hideAllPanels
hideAllPanels-method | hideAllPanels
hideNodes | hideNodes
hideNodes-method | hideNodes
hidePanel | hidePanel
hidePanel-method | hidePanel
hideSelectedEdges | hideSelectedEdges
hideSelectedEdges-method | hideSelectedEdges
hideSelectedNodes | hideSelectedNodes
hideSelectedNodes-method | hideSelectedNodes

## -- I --

initEdgeAttribute | initEdgeAttribute
initNodeAttribute | initNodeAttribute
invertEdgeSelection | invertEdgeSelection
invertEdgeSelection-method | invertEdgeSelection
invertNodeSelection | invertNodeSelection
invertNodeSelection-method | invertNodeSelection

## -- L --

layoutNetwork | layoutNetwork
layoutNetwork-method | layoutNetwork
lockNodeDimensions | lockNodeDimensions
lockNodeDimensions-method | lockNodeDimensions

## -- M --

makeRandomGraph | makeRandomGraph
makeSimpleGraph | makeSimpleGraph
msg | msg
msg-method | msg

## -- N --

new.CytoscapeWindow | new.CytoscapeWindow
noa | noa
noa.names | noa.names

## -- P --

ping | ping
ping-method | ping
pluginVersion | pluginVersion
pluginVersion-method | pluginVersion
predictTimeToDisplayGraph | predictTimeToDisplayGraph
predictTimeToDisplayGraph-method | predictTimeToDisplayGraph

## -- R --

raiseWindow | raiseWindow
raiseWindow-method | raiseWindow
redraw | redraw
redraw-method | redraw
restoreLayout | restoreLayout
restoreLayout-method | restoreLayout

## -- S --

saveImage | saveImage
saveImage-method | saveImage
saveLayout | saveLayout
saveLayout-method | saveLayout
saveNetwork | saveNetwork
saveNetwork-method | saveNetwork
selectEdges | selectEdges
selectEdges-method | selectEdges
selectFirstNeighborsOfSelectedNodes | selectFirstNeighborsOfSelectedNodes
selectFirstNeighborsOfSelectedNodes-method | selectFirstNeighborsOfSelectedNodes
selectNodes | selectNodes
selectNodes-method | selectNodes
sendEdges | sendEdges
sendEdges-method | sendEdges
sendNodes | sendNodes
sendNodes-method | sendNodes
setCenter | setCenter
setCenter-method | setCenter
setDefaultBackgroundColor | setDefaultBackgroundColor
setDefaultBackgroundColor-method | setDefaultBackgroundColor
setDefaultEdgeColor | setDefaultEdgeColor
setDefaultEdgeColor-method | setDefaultEdgeColor
setDefaultEdgeFontSize | setDefaultEdgeFontSize
setDefaultEdgeFontSize-method | setDefaultEdgeFontSize
setDefaultEdgeLineWidth | setDefaultEdgeLineWidth
setDefaultEdgeLineWidth-method | setDefaultEdgeLineWidth
setDefaultEdgeReverseSelectionColor | setDefaultEdgeReverseSelectionColor
setDefaultEdgeReverseSelectionColor-method | setDefaultEdgeReverseSelectionColor
setDefaultEdgeSelectionColor | setDefaultEdgeSelectionColor
setDefaultEdgeSelectionColor-method | setDefaultEdgeSelectionColor
setDefaultNodeBorderColor | setDefaultNodeBorderColor
setDefaultNodeBorderColor-method | setDefaultNodeBorderColor
setDefaultNodeBorderWidth | setDefaultNodeBorderWidth
setDefaultNodeBorderWidth-method | setDefaultNodeBorderWidth
setDefaultNodeColor | setDefaultNodeColor
setDefaultNodeColor-method | setDefaultNodeColor
setDefaultNodeFontSize | setDefaultNodeFontSize
setDefaultNodeFontSize-method | setDefaultNodeFontSize
setDefaultNodeLabelColor | setDefaultNodeLabelColor
setDefaultNodeLabelColor-method | setDefaultNodeLabelColor
setDefaultNodeReverseSelectionColor | setDefaultNodeReverseSelectionColor
setDefaultNodeReverseSelectionColor-method | setDefaultNodeReverseSelectionColor
setDefaultNodeSelectionColor | setDefaultNodeSelectionColor
setDefaultNodeSelectionColor-method | setDefaultNodeSelectionColor
setDefaultNodeShape | setDefaultNodeShape
setDefaultNodeShape-method | setDefaultNodeShape
setDefaultNodeSize | setDefaultNodeSize
setDefaultNodeSize-method | setDefaultNodeSize
setEdgeAttributes | setEdgeAttributes
setEdgeAttributes-method | setEdgeAttributes
setEdgeAttributesDirect | setEdgeAttributesDirect
setEdgeAttributesDirect-method | setEdgeAttributesDirect
setEdgeColorDirect | setEdgeColorDirect
setEdgeColorDirect-method | setEdgeColorDirect
setEdgeColorRule | setEdgeColorRule
setEdgeColorRule-method | setEdgeColorRule
setEdgeFontSizeDirect | setEdgeFontSizeDirect
setEdgeFontSizeDirect-method | setEdgeFontSizeDirect
setEdgeLabelColorDirect | setEdgeLabelColorDirect
setEdgeLabelColorDirect-method | setEdgeLabelColorDirect
setEdgeLabelDirect | setEdgeLabelDirect
setEdgeLabelDirect-method | setEdgeLabelDirect
setEdgeLabelOpacityDirect | setEdgeLabelOpacityDirect
setEdgeLabelOpacityDirect-method | setEdgeLabelOpacityDirect
setEdgeLabelRule | setEdgeLabelRule
setEdgeLabelRule-method | setEdgeLabelRule
setEdgeLabelWidthDirect | setEdgeLabelWidthDirect
setEdgeLabelWidthDirect-method | setEdgeLabelWidthDirect
setEdgeLineStyleDirect | setEdgeLineStyleDirect
setEdgeLineStyleDirect-method | setEdgeLineStyleDirect
setEdgeLineStyleRule | specify the line styles to be used in drawing edges
setEdgeLineStyleRule-method | specify the line styles to be used in drawing edges
setEdgeLineWidthDirect | setEdgeLineWidthDirect
setEdgeLineWidthDirect-method | setEdgeLineWidthDirect
setEdgeLineWidthRule | setEdgeLineWidthRule
setEdgeLineWidthRule-method | setEdgeLineWidthRule
setEdgeOpacityDirect | setEdgeOpacityDirect
setEdgeOpacityDirect-method | setEdgeOpacityDirect
setEdgeOpacityRule | setEdgeOpacityRule
setEdgeOpacityRule-method | setEdgeOpacityRule
setEdgeSourceArrowColorDirect | setEdgeSourceArrowColorDirect
setEdgeSourceArrowColorDirect-method | setEdgeSourceArrowColorDirect
setEdgeSourceArrowColorRule | Specify Rule for the Source Arrow Color
setEdgeSourceArrowColorRule-method | Specify Rule for the Source Arrow Color
setEdgeSourceArrowOpacityDirect | setEdgeSourceArrowOpacityDirect
setEdgeSourceArrowOpacityDirect-method | setEdgeSourceArrowOpacityDirect
setEdgeSourceArrowRule | specify the arrow types to be used at the end of an edge, at the 'source' node
setEdgeSourceArrowRule-method | specify the arrow types to be used at the end of an edge, at the 'source' node
setEdgeSourceArrowShapeDirect | setEdgeSourceArrowShapeDirect
setEdgeSourceArrowShapeDirect-method | setEdgeSourceArrowShapeDirect
setEdgeTargetArrowColorDirect | setEdgeTargetArrowColorDirect
setEdgeTargetArrowColorDirect-method | setEdgeTargetArrowColorDirect
setEdgeTargetArrowColorRule | Specify Rule for the Target Arrow Color
setEdgeTargetArrowColorRule-method | Specify Rule for the Target Arrow Color
setEdgeTargetArrowOpacityDirect | setEdgeTargetArrowOpacityDirect
setEdgeTargetArrowOpacityDirect-method | setEdgeTargetArrowOpacityDirect
setEdgeTargetArrowRule | specify the arrow types to be used at the end of an edge, at the 'target' node
setEdgeTargetArrowRule-method | specify the arrow types to be used at the end of an edge, at the 'target' node
setEdgeTargetArrowShapeDirect | setEdgeTargetArrowShapeDirect
setEdgeTargetArrowShapeDirect-method | setEdgeTargetArrowShapeDirect
setEdgeTooltipDirect | setEdgeTooltipDirect
setEdgeTooltipDirect-method | setEdgeTooltipDirect
setEdgeTooltipRule | setEdgeTooltipRule
setEdgeTooltipRule-method | setEdgeTooltipRule
setGraph | setGraph
setGraph-method | setGraph
setLayoutProperties | setLayoutProperties
setLayoutProperties-method | setLayoutProperties
setNodeAttributes | setNodeAttributes
setNodeAttributes-method | setNodeAttributes
setNodeAttributesDirect | setNodeAttributesDirect
setNodeAttributesDirect-method | setNodeAttributesDirect
setNodeBorderColorDirect | setNodeBorderColorDirect
setNodeBorderColorDirect-method | setNodeBorderColorDirect
setNodeBorderColorRule | setNodeBorderColorRule
setNodeBorderColorRule-method | setNodeBorderColorRule
setNodeBorderOpacityDirect | setNodeBorderOpacityDirect
setNodeBorderOpacityDirect-method | setNodeBorderOpacityDirect
setNodeBorderWidthDirect | setNodeBorderWidthDirect
setNodeBorderWidthDirect-method | setNodeBorderWidthDirect
setNodeBorderWidthRule | setNodeBorderWidthRule
setNodeBorderWidthRule-method | setNodeBorderWidthRule
setNodeColorDirect | setNodeColorDirect
setNodeColorDirect-method | setNodeColorDirect
setNodeColorRule | setNodeColorRule
setNodeColorRule-method | setNodeColorRule
setNodeFillOpacityDirect | setNodeFillOpacityDirect
setNodeFillOpacityDirect-method | setNodeFillOpacityDirect
setNodeFontSizeDirect | setNodeFontSizeDirect
setNodeFontSizeDirect-method | setNodeFontSizeDirect
setNodeHeightDirect | setNodeHeightDirect
setNodeHeightDirect-method | setNodeHeightDirect
setNodeImageDirect | setNodeImageDirect
setNodeImageDirect-method | setNodeImageDirect
setNodeLabelColorDirect | setNodeLabelColorDirect
setNodeLabelColorDirect-method | setNodeLabelColorDirect
setNodeLabelDirect | setNodeLabelDirect
setNodeLabelDirect-method | setNodeLabelDirect
setNodeLabelOpacityDirect | setNodeLabelOpacityDirect
setNodeLabelOpacityDirect-method | setNodeLabelOpacityDirect
setNodeLabelRule | setNodeLabelRule
setNodeLabelRule-method | setNodeLabelRule
setNodeOpacityDirect | setNodeOpacityDirect
setNodeOpacityDirect-method | setNodeOpacityDirect
setNodeOpacityRule | setNodeOpacityRule
setNodeOpacityRule-method | setNodeOpacityRule
setNodePosition | setNodePosition
setNodePosition-method | setNodePosition
setNodeShapeDirect | setNodeShapeDirect
setNodeShapeDirect-method | setNodeShapeDirect
setNodeShapeRule | setNodeShapeRule
setNodeShapeRule-method | setNodeShapeRule
setNodeSizeDirect | setNodeSizeDirect
setNodeSizeDirect-method | setNodeSizeDirect
setNodeSizeRule | setNodeSizeRule
setNodeSizeRule-method | setNodeSizeRule
setNodeTooltipRule | setNodeTooltipRule
setNodeTooltipRule-method | setNodeTooltipRule
setNodeWidthDirect | setNodeWidthDirect
setNodeWidthDirect-method | setNodeWidthDirect
setTooltipDismissDelay | setTooltipDismissDelay
setTooltipDismissDelay-method | setTooltipDismissDelay
setTooltipInitialDelay | setTooltipInitialDelay
setTooltipInitialDelay-method | setTooltipInitialDelay
setVisualStyle | setVisualStyle
setVisualStyle-method | setVisualStyle
setWindowSize | setWindowSize
setWindowSize-method | setWindowSize
setZoom | setZoom
setZoom-method | setZoom
sfn | selectFirstNeighborsOfSelectedNodes
sfn-method | selectFirstNeighborsOfSelectedNodes
showGraphicsDetails | showGraphicsDetails
showGraphicsDetails-method | showGraphicsDetails

## -- U --

unhideAll | unhideAll
unhideAll-method | unhideAll