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RCytoscape (version 1.22.0)
Display and manipulate graphs in Cytoscape
Description
Interactvive viewing and exploration of graphs, connecting R to Cytoscape.
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Version
Version
1.22.0
1.20.1
1.18.0
1.16.0
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Version
1.22.0
License
GPL-2
Maintainer
Paul Shannon
Last Published
January 27th, 2016
Functions in RCytoscape (1.22.0)
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getGraphFromCyWindow
getGraphFromCyWindow
fitSelectedContent
fitSelectedContent
getArrowShapes
getArrowShapes
saveNetwork
saveNetwork
eda.names
eda.names
getEdgeAttributeNames
getEdgeAttributeNames
clearMsg
clearMsg
clearSelection
clearSelection
getAttributeClassNames
getAttributeClassNames
deleteNodeAttribute
deleteNodeAttribute
getLayoutNameMapping
getLayoutNameMapping
getDefaultEdgeReverseSelectionColor
getDefaultEdgeReverseSelectionColor
floatPanel
floatPanel
getAllNodes
getAllNodes
getEdgeAttribute
getEdgeAttribute
CytoscapeConnectionClass-class
Class "CytoscapeConnectionClass"
invertNodeSelection
invertNodeSelection
setEdgeTargetArrowRule
specify the arrow types to be used at the end of an edge, at the 'target' node
getNodeSize
getNodeSize
noa.names
noa.names
getNodePosition
getNodePosition
pluginVersion
pluginVersion
ping
ping
saveLayout
saveLayout
setNodeColorRule
setNodeColorRule
CytoscapeWindowClass-class
Class "CytoscapeWindowClass"
getZoom
getZoom
fitContent
fitContent
deleteSelectedNodes
deleteSelectedNodes
setNodeBorderWidthDirect
setNodeBorderWidthDirect
restoreLayout
restoreLayout
new.CytoscapeWindow
new.CytoscapeWindow
raiseWindow
raiseWindow
getDefaultNodeSelectionColor
getDefaultNodeSelectionColor
getVisualStyleNames
getVisualStyleNames
cy2.edge.names
cy2.edge.names
getNodeAttribute
getNodeAttribute
existing.CytoscapeWindow
existing.CytoscapeWindow
getDefaultEdgeSelectionColor
getDefaultEdgeSelectionColor
addCyNode
addCyNode
hideSelectedNodes
hideSelectedNodes
getAllEdges
getAllEdges
setDefaultEdgeFontSize
setDefaultEdgeFontSize
deleteSelectedEdges
deleteSelectedEdges
setDefaultNodeFontSize
setDefaultNodeFontSize
setDefaultNodeColor
setDefaultNodeColor
getWindowID
getWindowID
unhideAll
unhideAll
setDefaultNodeBorderWidth
setDefaultNodeBorderWidth
sendEdges
sendEdges
sendNodes
sendNodes
setEdgeLabelOpacityDirect
setEdgeLabelOpacityDirect
getLayoutNames
getLayoutNames
getDefaultBackgroundColor
getDefaultBackgroundColor
setCenter
setCenter
setEdgeLineStyleRule
specify the line styles to be used in drawing edges
getViewCoordinates
getViewCoordinates
setNodeBorderOpacityDirect
setNodeBorderOpacityDirect
setEdgeLineWidthRule
setEdgeLineWidthRule
setNodeColorDirect
setNodeColorDirect
setDefaultNodeSelectionColor
setDefaultNodeSelectionColor
setNodeSizeRule
setNodeSizeRule
setEdgeLabelWidthDirect
setEdgeLabelWidthDirect
setNodeImageDirect
setNodeImageDirect
setEdgeAttributesDirect
setEdgeAttributesDirect
setNodePosition
setNodePosition
setEdgeSourceArrowShapeDirect
setEdgeSourceArrowShapeDirect
setEdgeFontSizeDirect
setEdgeFontSizeDirect
getSelectedEdgeCount
getSelectedEdgeCount
setNodeShapeDirect
setNodeShapeDirect
setEdgeOpacityRule
setEdgeOpacityRule
setEdgeAttributes
setEdgeAttributes
eda
eda
setDefaultNodeBorderColor
setDefaultNodeBorderColor
setNodeLabelDirect
setNodeLabelDirect
setNodeBorderWidthRule
setNodeBorderWidthRule
setNodeTooltipRule
setNodeTooltipRule
setNodeSizeDirect
setNodeSizeDirect
getWindowList
getWindowList
setVisualStyle
setVisualStyle
getNodeShapes
getNodeShapes
selectEdges
selectEdges
setTooltipInitialDelay
setTooltipInitialDelay
setEdgeTargetArrowColorDirect
setEdgeTargetArrowColorDirect
getFirstNeighbors
getFirstNeighbors
initNodeAttribute
initNodeAttribute
getNodeCount
getNodeCount
setDefaultNodeSize
setDefaultNodeSize
setEdgeTargetArrowColorRule
Specify Rule for the Target Arrow Color
saveImage
saveImage
setEdgeLineWidthDirect
setEdgeLineWidthDirect
makeSimpleGraph
makeSimpleGraph
setDefaultNodeShape
setDefaultNodeShape
getLayoutPropertyType
getLayoutPropertyType
predictTimeToDisplayGraph
predictTimeToDisplayGraph
setEdgeTooltipDirect
setEdgeTooltipDirect
hideAllPanels
hideAllPanels
setEdgeColorRule
setEdgeColorRule
setEdgeTargetArrowOpacityDirect
setEdgeTargetArrowOpacityDirect
setNodeBorderColorDirect
setNodeBorderColorDirect
setNodeBorderColorRule
setNodeBorderColorRule
setEdgeLabelColorDirect
setEdgeLabelColorDirect
setGraph
setGraph
setLayoutProperties
setLayoutProperties
setEdgeSourceArrowOpacityDirect
setEdgeSourceArrowOpacityDirect
setNodeOpacityDirect
setNodeOpacityDirect
setNodeLabelColorDirect
setNodeLabelColorDirect
setNodeLabelOpacityDirect
setNodeLabelOpacityDirect
setNodeShapeRule
setNodeShapeRule
setTooltipDismissDelay
setTooltipDismissDelay
setWindowSize
setWindowSize
createWindowFromSelection
createWindowFromSelection
createWindow
createWindow
deleteEdgeAttribute
deleteEdgeAttribute
getLayoutPropertyValue
getLayoutPropertyValue
invertEdgeSelection
invertEdgeSelection
layoutNetwork
layoutNetwork
hideNodes
hideNodes
setDefaultNodeLabelColor
setDefaultNodeLabelColor
setDefaultNodeReverseSelectionColor
setDefaultNodeReverseSelectionColor
CytoscapeConnection
CytoscapeConnection
getSelectedNodeCount
getSelectedNodeCount
CytoscapeWindow
CytoscapeWindow
getDirectlyModifiableVisualProperties
getDirectlyModifiableVisualProperties
getEdgeCount
getEdgeCount
getGraph
getGraph
getCenter
getCenter
getLayoutPropertyNames
getLayoutPropertyNames
hidePanel
hidePanel
makeRandomGraph
makeRandomGraph
getWindowCount
getWindowCount
msg
msg
redraw
redraw
getLineStyles
getLineStyles
setDefaultEdgeLineWidth
setDefaultEdgeLineWidth
setEdgeSourceArrowColorDirect
setEdgeSourceArrowColorDirect
setEdgeTooltipRule
setEdgeTooltipRule
setNodeFontSizeDirect
setNodeFontSizeDirect
setNodeAttributesDirect
setNodeAttributesDirect
setNodeFillOpacityDirect
setNodeFillOpacityDirect
setEdgeTargetArrowShapeDirect
setEdgeTargetArrowShapeDirect
setZoom
setZoom
setEdgeSourceArrowRule
specify the arrow types to be used at the end of an edge, at the 'source' node
setEdgeLineStyleDirect
setEdgeLineStyleDirect
addGraphToGraph
addGraphToGraph
deleteAllWindows
deleteAllWindows
demoSimpleGraph
demoSimpleGraph
deleteWindow
deleteWindow
dockPanel
dockPanel
getAllNodeAttributes
getAllNodeAttributes
getSelectedEdges
getSelectedEdges
hideSelectedEdges
hideSelectedEdges
addCyEdge
addCyEdge
getSelectedNodes
getSelectedNodes
copyVisualStyle
copyVisualStyle
noa
noa
selectNodes
selectNodes
selectFirstNeighborsOfSelectedNodes
selectFirstNeighborsOfSelectedNodes
lockNodeDimensions
lockNodeDimensions
displayGraph
displayGraph
setNodeAttributes
setNodeAttributes
getDefaultNodeReverseSelectionColor
getDefaultNodeReverseSelectionColor
setNodeHeightDirect
setNodeHeightDirect
getAdjacentEdgeNames
getAdjacentEdgeNames
setNodeLabelRule
setNodeLabelRule
initEdgeAttribute
initEdgeAttribute
getNodeAttributeNames
getNodeAttributeNames
setDefaultEdgeSelectionColor
setDefaultEdgeSelectionColor
setNodeWidthDirect
setNodeWidthDirect
setDefaultBackgroundColor
setDefaultBackgroundColor
setDefaultEdgeColor
setDefaultEdgeColor
setDefaultEdgeReverseSelectionColor
setDefaultEdgeReverseSelectionColor
setEdgeLabelRule
setEdgeLabelRule
setEdgeOpacityDirect
setEdgeOpacityDirect
setEdgeSourceArrowColorRule
Specify Rule for the Source Arrow Color
setEdgeLabelDirect
setEdgeLabelDirect
setNodeOpacityRule
setNodeOpacityRule
showGraphicsDetails
showGraphicsDetails
setEdgeColorDirect
setEdgeColorDirect
getAllEdgeAttributes
getAllEdgeAttributes