Is this part of a Shiny app? (if so, you might want to move this to #shiny to help others find your question)
Possibly worth checking out joe's talk, Linking HTML Widgets with Crosstalk.
In plotly you can create a big plot with lots of subplots which are connected to each other with the same data through the package crosstalk. It's all done at the javascript level so you don't need any shiny server for that.
Its very good for flex dashboard and markdowns. There is a section in @cpsievert git book about plotly and you can learn it in like half an hour.