cytoscape/cyjShiny

An R/shiny widget for cytoscape.js

cyjShiny

cyjShiny is a Shiny widget based on htmlwidgets for network visualization using cytoscape.js.

Installation

From CRAN (Stable Version)

Users should start with CRAN as it is the most stable version:

install.packages("cyjShiny") 

Install from GitHub (Development Version)

library(remotes)
remotes::install_github(repo="cytoscape/cyjShiny", ref="master", build_vignette=TRUE)

Compile cytoscape.js (Javascript Development)

Instructions for compiling cytoscape.js for use with htmlwidgets. NOTE: This should only be used by those actively modifying cytoscape.js.

Quick Start (First cyjShiny App)

• Shiny Development Basics
• Shiny Extensions for Embedding Javascript Visualizations
• Get Help: help(package="cyjShiny")
  • Main available features: layouts, node selection, styling, save to PNG, fit graphs to display area
• Quick Start Example:

library(shiny)
library(cyjShiny)
library(graph)
library(jsonlite)

# NETWORK DATA ----
tbl_nodes <- data.frame(id=c("A", "B", "C"), 
                        size=c(10, 20, 30),
                        stringsAsFactors=FALSE)

# Must have the interaction column 
tbl_edges <- data.frame(source=c("A", "B", "C"),
                        target=c("B", "C", "A"),
                        interaction=c("inhibit", "stimulate", "inhibit"),
                        stringsAsFactors=FALSE)

graph_json <- toJSON(dataFramesToJSON(tbl_edges, tbl_nodes), auto_unbox=TRUE)

# UI ----
ui <- fluidPage(cyjShinyOutput('cyjShiny'))

# SERVER ----
server <- function(input, output, session) {
  output$cyjShiny <- renderCyjShiny({
    # Layouts (see js.cytoscape.org): cola, cose, circle, concentric, grid, breadthfirst, random, fcose, spread
    cyjShiny(graph_json, layoutName="cola")
  })
}

# RUN ----
shinyApp(ui=ui, server=server)

Styling

Many of the visual properties of a network can be stylized.

• Styling Documentation
• Example Styling (data() maps data dynamically to specify a property value from the input data.frame):

[
  {"selector":"node", "css": {
    "border-width": "2px",
    "width": "data(size)",
    "height": "data(size)", 
    "content": "data(id)"
  }},
  {"selector": "edge[interaction='stimulate']", "css": {
    "line-color": "green"
  }},
  {"selector": "edge[interaction='inhibit']", "css": {
    "line-color": "red"
  }}
]

• Styling Usage with Quick Start Example:

Save the example styling to a file style.js in the current working directory and replace cyjShiny() in the Quick Start example as shown below:

cyjShiny(graph_json, layoutName="cola", styleFile="style.js")

Demos

• Try basicDemo Demo on shinyapps.io
• basicDemo Code
• Other Demos:
  • quickStartDemo: Demo used in README; Code
  • rmarkdownDemo: Demo for cyjShiny use in R Markdown files; Code
  • dataFrameGraphWithPresetNodePositions: Use preset layout to set node positions; Code
  • fromCytoscapeDesktop: Load and visualize networks generated in Cytoscape Desktop; Code
  • saveAndRestoreLayout: Within a session, save node positions and restore positions for nodes moved after positions saved; Code
  • withDT: Include at DT table of node values along with the graph visualization; Code