Syntax highlighting for Python chunks does not work

Question

I'm trying to create notebooks in which I present the same algorithm written in R and Python. I can easily integrate the R and Python code in a Rmd file and then create a HTML output using the 'Knit HTML' button in RStudio. However the Python code is always displayed without syntax highlighting (not like in the example at https://github.com/yihui/knitr-examples/blob/master/023-engine-python.md). I have Andre Simon's highlight software installed and functioning on my computer (MacBook Pro Retina, MacOS X 10.9).

Currently, I have the following libraries installed in R: markdown 0.6.4, knitr 1.5.15, highr 0.3.1.

Any idea what could be the problem? Thanks for your help!.

Keri

Answer 1

That is specific to the RStudio Markdown render, which did not enable syntax highlighting for code blocks that are not R or C++. RStudio uses highlight.js, and you can use your own version of highlight.js to highlight Python code. Or use other Markdown converters such as Pandoc.

Tsuda

Thanks! Pandoc did the trick. Now I need to learn how it works to get the result I want :-) – Keri

Can you add a simple example how to use pandoc to enable the code highlighting for a .Rmd doc containing both R and Python chuncks? I am working with Rstudio and want to enable syntax highlighting for python chuncks. – Lilli

@Lilli Just use '''py and ''' to include your Python code (replace ' with a backtick, since I cannot type a literal backtick here). – Tsuda

@Yihui: I solved it by adding the following to the output as defined in the .Rmd in Rstudio: html_document: theme: united toc: true toc_depth: 4 number_sections: true highlight: pygments (see geoscripting-wur.github.io/PythonWeek) – Lilli