options(width=120) knitr::opts_chunk$set( collapse = TRUE, eval=interactive(), echo=TRUE, comment = "#>" )
cyjShiny is a Shiny widget based on htmlWidgets for network visualization using cytoscape.js.
install.packages("cyjShiny")
Demo files are files in inst/demos
folder of the project code repository: https://github.com/cytoscape/cyjShiny
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")
Many of the visual properties of a network can be stylized.
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" }} ]
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)
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)
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)
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")
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)
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