figure captions, references using knitr and markdown to html

Question

I'm writing an Rmd file, to be processed by knitr into HTML. It contains some R chunks that generate figures, which get stored as data URIs in HTML.

1) How do I add a caption to such an image? I'd like to have a caption that says something like "Figure 3: blah blah blah", where the "3" is automatically generated.

2) How do I later on reference this image, i.e., "as you can see in Figure 3, blah blah".

Answer 1

I'm late to the party, but I wanted to mention a small package I recently built to do figure captioning and cross-referencing with knitr. It is called kfigr and you can install it using devtools::install_github('mkoohafkan/kfigr'). It is still in active development but the main functionality is there. Be sure to check out the vignette, it shows some usage examples and defines some hooks for figure captions and anchors (I may later choose to have the package import knitr and define those hooks on load).

EDIT: kfigr is now available on CRAN!