Consolidate code that appears in both app and markdown

[rmbielby]

There's a bunch of duplication of code that's come in with the way we've put together the markdown code in the first place, with copying and pasting code from the shiny app. Would be better to have these duplications pulled out into a separate script of functions that can then be called by both the app and the markdown. Will improve reliability and consistency.

Main subtlety I can think of off the top of my head is the hardwired image sizes in the markdown, so would just need to add a flag in the function call to account for that.

[rmbielby]

May be needed as part of speeding up download.