cyjShiny Introduction

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)