I'm in exactly the same boat here, and agree that a Lakbey>R report>knitr>plotly workflow would be fantastic. Have you made any progress on the HTML issues? We do a ton of analysis delivered as markdown (on NGS data), and would love to have this functionality right within labkey where all the data lives. I've made the decision to stick with implementation in R vs. translating to using labkey's internal visualization tools because we're often plotting thousands of points, with complex grouping (also mentioned above) -- plot.ly/ggplot seems to be the trick, but can't get it working within the knitr R view. Additionally, the htmlwidgets offer some great interactivity as well, seems like there are just some hurdles to get the JS to place nicely with labkey.

I do have a way around this however, and managed to configure the wiki view to point to a shiny application vis some JS in the source tab. As long as the shiny server can see the same data as your labkey study data, they don't even need to be on the same server, and the user doesn't know the difference -- they just see the shiny application running from within labkey. That said, because the markdown documents are so portable, would be great to get some interactive functionality within the markdown document itself.

-daniel