Display and manipulate graphs in cytoscape.js


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Documentation for package ‘RCyjs’ version 2.14.0

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A C D E F G H I L N R S V misc

-- A --

addGraph addGraph
addGraph-method addGraph
addGraphFromFile addGraphFromFile
addGraphFromFile-method addGraphFromFile

-- C --

clearSelection clearSelection
clearSelection-method clearSelection
createTestGraph createTestGraph

-- D --

dataFramesToJSON Create a cytoscape.js JSON graph from one or two data.frames.
deleteGraph deleteGraph
deleteGraph-method deleteGraph
deleteSelectedNodes deleteSelectedNodes
deleteSelectedNodes-method deleteSelectedNodes

-- E --

eda eda
edaNames edaNames

-- F --

fit fit
fit-method fit
fitSelection fitSelection
fitSelection-method fitSelection

-- G --

getEdgeCount getEdgeCount
getEdgeCount-method getEdgeCount
getJSON getJSON
getJSON-method getJSON
getLayoutStrategies getLayoutStrategies
getLayoutStrategies-method getLayoutStrategies
getNodeCount getNodeCount
getNodeCount-method getNodeCount
getNodes getNodes
getNodes-method getNodes
getPosition getPosition
getPosition-method getPosition
getSelectedNodes getSelectedNodes
getSelectedNodes-method getSelectedNodes
getSupportedEdgeDecoratorShapes getSupportedEdgeDecoratorShapes
getSupportedEdgeDecoratorShapes-method getSupportedEdgeDecoratorShapes
getSupportedNodeShapes getSupportedNodeShapes
getSupportedNodeShapes-method getSupportedNodeShapes
getZoom getZoom
getZoom-method getZoom
graphNELtoJSON.string Convert R graphNEL object to cytoscape.js JSON.

-- H --

hAlign hAlign
hAlign-method hAlign
hideAllEdges hideAllEdges
hideAllEdges-method hideAllEdges
hideEdges hideEdges
hideEdges-method hideEdges
hideNodes hideNodes
hideNodes-method hideNodes
hideSelectedNodes hideSelectedNodes
hideSelectedNodes-method hideSelectedNodes

-- I --

invertNodeSelection invertNodeSelection
invertNodeSelection-method invertNodeSelection

-- L --

layout layout
layout-method layout
layoutSelectionInGrid layoutSelectionInGrid
layoutSelectionInGrid-method layoutSelectionInGrid
layoutSelectionInGridInferAnchor layoutSelectionInGridInferAnchor
layoutSelectionInGridInferAnchor-method layoutSelectionInGridInferAnchor
loadStyleFile loadStyleFile
loadStyleFile-method loadStyleFile

-- N --

noa noa
noaNames noaNames

-- R --

RCyjs Create an RCyjs object
RCyjs-class Create an RCyjs object
readAndStandardizeJSONNetworkFile Read in a JSON network file, identify (or add) elements field return JSON
readAndStandardizeJSONStyleFile Read in a JSON file, extract the selector elements, return JSON
redraw redraw
redraw-method redraw
restoreLayout restoreLayout
restoreLayout-method restoreLayout

-- S --

saveJPG saveJPG
saveJPG-method saveJPG
saveLayout saveLayout
saveLayout-method saveLayout
savePNG savePNG
savePNG-method savePNG
selectFirstNeighborsOfSelectedNodes selectFirstNeighborsOfSelectedNodes
selectFirstNeighborsOfSelectedNodes-method selectFirstNeighborsOfSelectedNodes
selectNodes selectNodes
selectNodes-method selectNodes
setBackgroundColor setBackgroundColor
setBackgroundColor-method setBackgroundColor
setDefaultEdgeColor setDefaultEdgeColor
setDefaultEdgeColor-method setDefaultEdgeColor
setDefaultEdgeLineColor setDefaultEdgeLineColor
setDefaultEdgeLineColor-method setDefaultEdgeLineColor
setDefaultEdgeLineStyle setDefaultEdgeLineStyle
setDefaultEdgeLineStyle-method setDefaultEdgeLineStyle
setDefaultEdgeSourceArrowColor setDefaultEdgeSourceArrowColor
setDefaultEdgeSourceArrowColor-method setDefaultEdgeSourceArrowColor
setDefaultEdgeSourceArrowShape setDefaultEdgeSourceArrowShape
setDefaultEdgeSourceArrowShape-method setDefaultEdgeSourceArrowShape
setDefaultEdgeTargetArrowColor setDefaultEdgeTargetArrowColor
setDefaultEdgeTargetArrowColor-method setDefaultEdgeTargetArrowColor
setDefaultEdgeTargetArrowShape setDefaultEdgeTargetArrowShape
setDefaultEdgeTargetArrowShape-method setDefaultEdgeTargetArrowShape
setDefaultEdgeWidth setDefaultEdgeWidth
setDefaultEdgeWidth-method setDefaultEdgeWidth
setDefaultNodeBorderColor setDefaultNodeBorderColor
setDefaultNodeBorderColor-method setDefaultNodeBorderColor
setDefaultNodeBorderWidth setDefaultNodeBorderWidth
setDefaultNodeBorderWidth-method setDefaultNodeBorderWidth
setDefaultNodeColor setDefaultNodeColor
setDefaultNodeColor-method setDefaultNodeColor
setDefaultNodeFontColor setDefaultNodeFontColor
setDefaultNodeFontColor-method setDefaultNodeFontColor
setDefaultNodeFontSize setDefaultNodeFontSize
setDefaultNodeFontSize-method setDefaultNodeFontSize
setDefaultNodeHeight setDefaultNodeHeight
setDefaultNodeHeight-method setDefaultNodeHeight
setDefaultNodeShape setDefaultNodeShape
setDefaultNodeShape-method setDefaultNodeShape
setDefaultNodeSize setDefaultNodeSize
setDefaultNodeSize-method setDefaultNodeSize
setDefaultNodeWidth setDefaultNodeWidth
setDefaultNodeWidth-method setDefaultNodeWidth
setDefaultStyle setDefaultStyle
setDefaultStyle-method setDefaultStyle
setEdgeAttributes setEdgeAttributes
setEdgeAttributes-method setEdgeAttributes
setEdgeStyle setEdgeStyle
setEdgeStyle-method setEdgeStyle
setGraph setGraph
setGraph-method setGraph
setNodeAttributes setNodeAttributes
setNodeAttributes-method setNodeAttributes
setNodeBorderColor setNodeBorderColor
setNodeBorderColor-method setNodeBorderColor
setNodeBorderWidth setNodeBorderWidth
setNodeBorderWidth-method setNodeBorderWidth
setNodeColor setNodeColor
setNodeColor-method setNodeColor
setNodeColorRule setNodeColorRule
setNodeColorRule-method setNodeColorRule
setNodeFontColor setNodeFontColor
setNodeFontColor-method setNodeFontColor
setNodeFontSize setNodeFontSize
setNodeFontSize-method setNodeFontSize
setNodeHeight setNodeHeight
setNodeHeight-method setNodeHeight
setNodeLabelAlignment setNodelLabelAlignment
setNodeLabelAlignment-method setNodelLabelAlignment
setNodeLabelRule setNodeLabelRule
setNodeLabelRule-method setNodeLabelRule
setNodeShape setNodeShape
setNodeShape-method setNodeShape
setNodeSize setNodeSize
setNodeSize-method setNodeSize
setNodeSizeRule setNodeSizeRule
setNodeSizeRule-method setNodeSizeRule
setNodeWidth setNodeWidth
setNodeWidth-method setNodeWidth
setPosition setPosition
setPosition-method setPosition
setZoom setZoom
setZoom-method setZoom
sfn sfn
sfn-method sfn
showAll showAll
showAll-method showAll
showEdges showEdges
showEdges-method showEdges
showNodes showNodes
showNodes-method showNodes
simpleDemoGraph simpleDemoGraph

-- V --

vAlign vAlign
vAlign-method vAlign

-- misc --

.RCyjs Create an RCyjs object