Introduction

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

Installation

install.packages("cyjShiny")

Demo Files

Demo files are files in inst/demos folder of the project code repository: https://github.com/cytoscape/cyjShiny

Quick Start Example

Running the following code in RStudio will produce output in the Viewer panel
Running this code as an RMarkdown chunk will embed the cyjShiny network visualization into the document

library(cyjShiny)

# 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)

# graph_json is a string with JSON content that is input to cytoscape.js
print(graph_json)

cyjShiny(graph=graph_json, layoutName="cola")

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:

style_file <- system.file(file.path("demos", "rmarkdownDemo", "style.js"), package="cyjShiny")
cyjShiny(graph_json, layoutName="cola", styleFile=style_file)

Layouts

Cytoscape.js includes many layouts by default, including: cola, cose, circle, concentric, grid, breadthfirst, random, fcose, spread, preset

yeast_galactose_style_file <- system.file(file.path("demos", "rmarkdownDemo", "yeastGalactoseStyle.js"), package="cyjShiny")
yeast_galactose_graph <- readLines(system.file(file.path("demos", "rmarkdownDemo", "yeastGalactose.cyjs"), package="cyjShiny"))

cyjShiny(yeast_galactose_graph, layoutName="fcose", styleFile=yeast_galactose_style_file)

Preset Layout

The preset layout can be used to retain a layout

style_file <- system.file(file.path("demos", "rmarkdownDemo", "preset_style.js"), package="cyjShiny")
graph_json <- readLines(system.file(file.path("demos", "rmarkdownDemo", "preset_graph.js"), package="cyjShiny"))
cyjShiny(graph_json, layoutName="preset", styleFile=style_file)

cyjShiny and Cytoscape Desktop

Networks from the Cytoscape Desktop can also be visualized within cyjShiny. Users can export the network for use with cytoscape.js (cyjShiny-compatible) format in this way:

File -> Export -> Network to File -> Export File Format: "Cytoscape.js JSON (*.js)"

Any layouts generated in Cytoscape Desktop can be retained in cyjShiny by using the preset layout as shown in the example.

preset_graph_file <- system.file(file.path("demos", "fromCytoscapeDesktop", "small", "cyjshiny.cyjs"), package="cyjShiny")
graph_json <- readAndStandardizeJSONNetworkFile(preset_graph_file)
writeLines(graph_json, "cyjshiny_cytoscape_desktop.cyjs")

cyjShiny(graph_json, layoutName="preset")

cyjShiny as Part of Shiny Applications

The following code create a minimal R Shiny application with network visualization using cyjShiny and cytoscape.js.

> 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)

cyjShiny Introduction