If I understood you correctly, you could at least do this using HTML output, as in this minimal example:
--- title: "Toggle Code boxes" output: html_document date: "January 12, 2016" --- First add the javascript to toggle boxes(remember to indent it) <script language="javascript"> function toggle(num) { var ele = document.getElementById("toggleText" + num); var text = document.getElementById("displayText" + num); if(ele.style.display == "block") { ele.style.display = "none"; text.innerHTML = "show"; } else { ele.style.display = "block"; text.innerHTML = "hide"; } } </script> and then we have some R code with the toggle button wrapped around (also indented): <a id="displayText" href="javascript:toggle(1);">Show underlying code</a> <div id="toggleText1" style="display: none"> ```{r} x <- sample(100) mean.x <- mean(x) ``` </div> The mean is `r mean.x`. Please click the link to see the source code. <a id="displayText" href="javascript:toggle(2);">Show underlying code</a> <div id="toggleText2" style="display: none"> ```{r} median.x <- median(x) ``` </div> And the median is `r median.x`. Please click the link to see the source code.