After some delay (and because of helpful prompting by Giles Heywood and code contributions by John Harrison) d3Network now plays nicely with Shiny web apps. This means you can fully integrate R/D3.js network graphs into your web apps.
Here is what one simple example looks like:
An explanation of the code is here and you can download the app and play with it using:
shiny::runGitHub('d3ShinyExample', 'christophergandrud')<br />