Today I wrote javascript code to do the data format transformations and was able to use plotly.js directly. While it did not take a lot of code, it took a while for me to get it right. Transforming the data for a simple scatter plot is easy, but plots involving grouping are more involved. The d3 library, and in particular d3.nest(), turned out to be very useful but also has a bit of a learning curve. I might post some code once I do some refactoring.

I still think the Lakbey>R report>knitr>plotly approach will be useful for opening up plotly to more users, and I plan to spend some more time looking into the knitr HTML escaping issue.

-Will