# Cytoscape.js Shiny Widget (cyjShiny)

## Documentation for package ‘cyjShiny’ version 1.0.42

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

## Help Pages

addGraphFromDataFrame | Add graph from data.frame
addGraphFromJsonFile | Add graph from JSON file
clearSelection | Clear selection all node and edge selections removed
cyjShiny | cyjShiny cyjShiny
cyjShinyOutput | Standard shiny ui rendering construct
dataFramesToJSON | Create a cytoscape.js JSON graph from one or two data.frames.
doLayout | Layout the current graph using the specified strategy.
fit | Set zoom and center of the graph display so that graph fills the display.
fitSelected | Set zoom and center of the graph display so that the currently selected nodes fill the display
getNodePositions | Get node positions
getSelectedNodes | Get Selected Nodes
graphNELtoJSON | Convert R graphNEL object to cytoscape.js JSON.
hideSelection | Hide selection all selected nodes and their edges are hidden
invertSelection | Invert selection all selected nodes and their edges are hidden
loadNetworkFromJSONFile | Load a standard cytoscape.js JSON network file
loadStyleFile | Load a standard cytoscape.js style file
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
removeGraph | Remove the current graph
renderCyjShiny | More shiny plumbing - a cyjShiny wrapper for htmlwidget standard rendering operation
savePNGtoFile | Save a png rendering of the current network view to the specified filename
selectFirstNeighbors | Select first neighbors of the currently selected nodes
selectNodes | Select Nodes
setEdgeAttributes | Assign the supplied edge attribute values to the graph structure contained in the browser.
setNodeAttributes | Assign the supplied node attribute values to the graph structure contained in the browser.
setNodePositions | Set node positions from the supplied data.frame
showAll | Show all all selected nodes and their edges are hidden