Changing Style – knitr and markdown in RStudio

Knitr support in RStudio is a nice but the default styling of the HTML output, in particular the treatment of tables, is not to my taste. It is possible to override the default handler for markdown, as described on the RStudio site, but this doesn’t immediately work when using knitr in RStudio as several posts to stackoverflow etc testify (with some interesting workarounds proposed involving post-processing the output). This blog post (Neil Saunders) explains how to make it work but requires sourcing a file manually.

Having finally worked it out, I’m pleased to say the answer is simple.

Create a file named .Rprofile in the same directory as your RStudio project with the following contents:

options(rstudio.markdownToHTML = 
  function(inputFile, outputFile) {      
    markdownToHTML(inputFile, outputFile, stylesheet='custom.css')   

Grab a copy of the default CSS and save it to the project directory. Edit to your taste. For example, adopt Neil Saunders’ table style to replace the existing table style specification:

table {
  max-width: 95%;
  border: 1px solid #ccc;
th {
  background-color: #000000;
  color: #ffffff;
td {
  background-color: #dcdcdc;

Close and re-open RStudio (or the project), which will execute the contents of .Rprofile. This must happen prior to starting the markdown processor, which is why you cannot just set this option within the .Rmd.

I hope this saves someone the time I spent hunting for the solution… and not finding the simple recipe.

Kudos to Yihui Xie for knitr. It is great stuff and being actively maintained.

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2 thoughts on “Changing Style – knitr and markdown in RStudio

  1. You can also take a look at the ‘header’ argument in markdownToHTML(), which is better if you only need to make a slight modification of the CSS, because you will not have to copy the whole markdown.css

  2. There is a problem with the method described here, and implicit in Yihui’s alternative suggestion. Both make use of the markdown package. The purpose of the content in the .Rprofile file that I gave above is to make RStudio use markdown rather than its own mechanism (derived from the same original code as markdown, I believe).

    One of the extensions provided by the Rstudio version is to handle latex style maths equations – e.g. $P(E) = {n \choose k} p^k (1-p)^{n-k}$ – and to produce HTML that uses the MathJax Javascript library to render it in the browser.

    This appears to give you a choice: control over style OR nice equation rendering.

    A global workaround is to replace the CSS in the RStudio installation. For me on Ubuntu Linux, this is in /usr/lib/rstudio/resources.

    I don’t like hacking in the installation directory and it reduces portability. The only other alternative appears to be to insert an HTML style block at the top of each markdown file. Thats a bit ugly too.

    Cheers, Adam

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