RBioFabric

An R implementation of the BioFabric network visualization tool by William Longabaugh (@wjrl)

This fork is almost entirely code from the original source, but this forked version is an attempt to add an interactive htmlwidget BioFabric visualization directly from R. It will leverage the functionality of bioFabric and all the power of igraph. This is highly experimental, but it does work. If you would like to try, here is some code.

Most of the remaining work is adding helpful interactivity on the d3.js/JavaScript side. Thankfully, @maxogden had started generalizing @wjrl's JavaScript here. So far, I have been able to add crude pan/zoom, better sizing, and a first pass at helpful mouseover interactivity.

Installation

RBioFabric is not on CRAN, so please install with devtools.

devtools::install_github("timelyportfolio/RBioFabric")

Examples

Here are a couple examples.

#devtools::install_github("timelyportfolio/RBioFabric")

library(igraph)
library(RBioFabric)

# d3 example from BioFabric
#  source:   https://github.com/wjrl/D3BioFabric
#  example:  http://rawgit.com/wjrl/D3BioFabric/master/src/JustBioFabric.html

miserables <- jsonlite::fromJSON(
  "https://rawgit.com/wjrl/D3BioFabric/master/src/data/miserablesSimple.json"
)

mis_igraph <- graph.data.frame(
  d = miserables$links
  ,vertices = data.frame(
    id = as.character( 0:(nrow(miserables$nodes)-1) ) 
    ,name = miserables$nodes
    ,stringsAsFactors = F
  )
)

bioFabric_htmlwidget( bioFabric( mis_igraph ) )

library(igraph)
library(igraphdata)
library(RBioFabric)

data(Koenigsberg)

bioFabric_htmlwidget( bioFabric( Koenigsberg ) )