I cannot figure out how to arrange two side-by-side plots as explained in the knitr graphics manual page 2 (http://yihui.name/knitr/demo/graphics/). I use the following MWE
An alternative which worked for me: save the plots as files, then put the picture markdown on the same line (from here).
## Show images
 
You can save ggplot plot objects with ggsave.
Base plots are a bit more complicated, see for example here.
I'm putting this answer here because it helped me. Whether it's better for you or not depends on your situation.