# Display and manipulate graphs in cytoscape.js

## Documentation for package ‘RCyjs’ version 2.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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