hooks for knitr when I wrote my crime.html spatial stats tutorial. The main hook puts the code and image into separate divs. Written a couple of years ago as part of a more complex build system...

hooks.R

hook=list()
hook$plot = function(x,options){
  sprintf("\n[[[%s]]]\n",knitr:::.upload.url(x))
}

imgmodal <- function(url,name){
sprintf('<a  data-toggle="modal" href="#img-%s" >
<img src="%s" class="rplot" />
</a>
    <div class="modal hide fade" id="img-%s">
    <button class="close" data-dismiss="modal">×</button>
    <img src="%s" />
    <a href="" class="btn btn-primary" data-dismiss="modal">Close</a>
    </div> ',name,url,name,url)
}


hook$chunk=
function (x, options) 
{
  if (knitr:::output_asis(x, options)) 
    return(x)
  ## find the images
  lines = strsplit(x,"\n")[[1]]
  gotImage = grep("^\\[\\[\\[(.*)\\]\\]\\]$",lines)
  if(length(gotImage)>0){
    figs = lines[gotImage]
    lines = lines[-gotImage]
    urls = substring(figs,4,nchar(figs)-3)
    imgs = imgmodal(urls,options$label) #sprintf("<img src=\"%s\" />",urls)
    imgdiv = sprintf("<div class=\"rimage\">%s</div>",paste(imgs,collapse=""))
    tclass="transcript half"
  }else{
    imgdiv=""
    tclass="transcript" # full width transcript
  }
  transcript = sprintf("<div class=\"%s\">%s</div>\n",tclass,paste(lines,collapse="\n"))
  x = sprintf("<div id=\"%s\" class=\"chunk\">%s</div>", options$label, paste(transcript,imgdiv))
  if (options$split) {
    cat("split...\n")
    name = fig_path(".html", options)
    if (!file.exists(dirname(name))) 
      dir.create(dirname(name))
    cat(x, file = name)
    sprintf("<iframe src=\"%s\" class=\"knitr\" width=\"100%%\"></iframe>", 
            name)
  }
  else x
}

render_html()
knit_hooks$set(hook)