Plotly has turned into my go to shiny data viz tool. The R package is open source and installable via CRAN or https://github.com/ropensci/plotly. In addition to providing a nice API for interacting with the JavaScript plotly library, it also has the function ggplotly that lets you stick in a plot created by ggplot2 (though more advanced plots sometimes lose little bits of functionality with the generated tooltips).
There are a bunch of other R to JavaScript libraries out there -- see http://gallery.htmlwidgets.org for a huge list -- and I've tried dozens of them, but plotly has just gotten better and better over the past couple years and the MIT license means I can do whatever I want with it.