Putting line number for R code with knitr

Question

I wonder if there is any function to put line numbers with knitr in .Rnw. I found this discussion and some documents (now removed from the web) but could not find the way to put line numbers.

Gromme

To clarify, you want line numbers in the pdf output? Or in the .Rnw file? – Chapen

Yes, I need line numbers in pdf output. – Gromme

And you want them for every line of the document or just line numbers in the chunk output? – Chapen

If you want line numbers for everything and are using Latex, then take a look at this solution: tex.stackexchange.com/a/18776 – Rickie

How about the solution here? https://mcmap.net/q/873576/-how-to-display-line-numbers-for-code-chunks-in-rmarkdown-html-and-pdf – Rickie

Thanks @RichieCotton for your efforts. Same problem has been mentioned in the link without any solution. – Gromme

Answer 1

This solution uses the LaTeX listings package to create line numbers. I can only get them to work by accumulating across all code chunks, but I imagine there is a similar solution that will enumerate lines only within each chunk. Here's the .Rnw source:

\documentclass{article}
\usepackage{listings}
\begin{document}

<<setup, echo=FALSE>>=
knit_hooks$set(source = function(x, options) {
    paste("\\begin{lstlisting}[numbers=left, firstnumber=last]\n", x, 
        "\\end{lstlisting}\n", sep = "")
})
@

<<a, results='hold'>>=
1:2
3:4
5:6
@

<<b>>=
"test1"
"test2"
"test3"
@

\end{document}

The key parts of this are in the source hook, which is basically copied from here. The firstnumber=last tells listings to accumulate line numbers across listings. Without it, all lines are numbered 1 because knitr is putting each code line in its own listing.

And here's the result:

If you want each code block to start numbering from 1, add a hook to reset the counter:

knit_hooks$set(reset = function(before, options, envir){
if(before){
    return("\\setcounter{lstnumber}{1}")
}
})

and then use reset=TRUE to activate the hook in each chunk you want:

<<a, results='hold', reset=TRUE>>=
1:2
3:4
@

Ascariasis

(+1): This is great @Thomas. Would be nice if line numbers change within each R Chunk. – Gromme

This works fine. But it is not getting the code (font) color as with original 'knitrout'. Any solution for that. – Gromme

@Gromme You should be able to add language=R to the listings options (i.e., where it says numbers=left, firstnumber=last). You my have to go through the listings manual to understand how to gain fine control over the highlighting. – Ascariasis

Any chance of customizing the rendering of the line numbers (i.e. lower font size)? Thanks. – Hajj

Answer 2

When using knitr with Lyx or Latex, I've found it helpful to add the lineno package to the document pre-amble and then to enclose the chunk with the \internallinenumbers \resetlinenumber[13].

Here's a minimal example:

\usepackage{lineno}

then in the body text, add the following before the code chunk:

{\internallinenumbers \resetlinenumber[13]

and then this after the code chunk:

}

With LyX (what I use for rapid LaTeX generation), I simply go to the document menu, then Settings->LaTeX Preamble and I add \usepackage{lineno}, click Apply, OK, and then Close. Then in the main document before my code chunk, I insert LaTeX source by clicking the "TEX" button menu button or by pressing "Ctrl+L" on the keyboard. Then I paste in {\internallinenumbers \resetlinenumber[13]. Finally, I place the cursor immediately after the code chunk and do the same thing. only I close the line numbering with a curly brace: }.

Here is a minimal example, when the code is in place is pasted below:

\documentclass[english]{article}
\usepackage{lineno}
\begin{document}
First line in main document before code chunk.

{\internallinenumbers \resetlinenumber[13]

<<CodeBlock1, highlight=TRUE, eval=FALSE, size="small">>=
x<-rnorm(10)
mean(x)
@
}
\end{document}

Aromaticity

Answer 3

For use in HTML, you can set the chunk option class.source to pass custom css to the output:

```{r class.source = c("numCode", "R", "numberLines")}
# your code
```

Gibbosity

The question is about Rnw (Sweave), not Rmd (Rmarkdown). – Unceasing