I have written some custom R code that wraps a third-party binary. One of that binary's features is to produce a LaTeX document with a figure and some text. One of my code's features is to parse that document and return the LaTeX code for the figure.
The goal is to embed my R code in an Rnw document. When Sweave is run, I want my code to produce a document using the third-party binary, then extract the LaTeX code for the figure and drop it into Sweave's .tex output. Then when I run latex against that output the figure that was generated by the third-party binary should appear, automagically and nicely formatted, in my report.
Instead, the LaTeX code is printed out like this:
[1] " %\\begin{landscape}"
[1] " \\begin{center}"
[1] "\\psset{linecolor=black,tnsep=2pt,tnheight=0cm,treesep=.3cm,levelsep=40pt,radius[1] "% \\def\\psedge#1#2{\\ncangle{#2}{#1}}"
[1] "% \\pstree[treemode=R]"
[1] " \\pstree{\\Tcircle{ 1 }~[tnpos=l]{\\shortstack[r]{nwsprec\\\\$\\leq$ 1.93}}}{"
And so on...
Is there a way to make Sweave treat R's output as LaTeX code?
Thanks in advance.
-Wesley
I figured it out! The Sweave code needs to look like this:
<<echo=False, results=tex, include=True>>=
...R code goes here...
#
Where the option results=tex is the crucial change that tells Sweave to interpret the output from R as LaTeX code.
And to get rid of the quotes and line numbers, I needed to use cat command in R rather than print. Specifically, I changed print(line) to cat( paste(line, "\n", sep='') ).
Related
I need to expose a markdown syntax, for figures, i.e. "! [caption] (imagepath)".
If you write it as-is, it will be interpreted and rendered by markdown.
Same appears to be true, if you generate the syntax from an R chunk.
What is the best way to achieve this result in a R markdown file ?
r '' # works but displays nothing
r '! [caption] (imagepath)' # works, based on a visible hack as spaces are not so easy to capture for human eyes
Actual result with visual hack is "! [caption] (imagepath)". Perfect result should be the same without spaces and without markdown interpretation.
You can put it in backticks:
``
You can easily make a whole markdown chunk not to be interpreted by adding:
eval = FALSE to it.
so
{r ,eval=FALSE}
''
creates the output:
[1] ""
I'm generating a knitr (focusing on .Rmd files) manual for a project and wanted to embed a code chunk that actually displays the " ``` " marks as well as the internal chunk syntax. E.g.
``` {r sample, eval= FALSE}
Code example
```
So basically the exact visual you see above. Any thoughts on how to do this?
You can do this by using four spaces before your code as follows:
So this:
Becomes this:
There also is this SO-meta discussion on how to escape this backtick in Markdown
If you mean how to display the three backticks, the answer is "indent by 4 spaces" (see Pandoc's four-space rule)". If you mean how to display a literal knitr code chunk, the answer has been given by knitr FAQ #8.
I had ask a similar question to this with respect to Sweave (
Dynamic references to figures in a R comment within Sweave document
) and would like to see if anyone as a similar answer when using knitr.
The goal is to have the following code chunk
<<"example", fig.cap = "some figure", highlight = FALSE>>=
# the following code generated Figure \ref{fig:example}
plot(1:10, 1:10)
#
have be displayed in the resulting .pdf as
# the following code generated Figure 1.1
plot(1:10, 1:10)
So far I have found that by setting highlight = FALSE the R code is placed into a verbatim environment in the resulting .tex file. If the environment could be alltt instead of verbatim then we'd have the desired output. Is it possible to have the non-highlighted code chunks be placed in alltt environments via a knitr option?
I have added an example 072-latex-reference.Rnw in the knitr-examples repository. The basic idea is to restore the escaped \ref{} (which should have been \textbackslash{}ref\{\} in the default output).
I'd like to use a Knitr/Sweave in-line call (\Sexpr{}) in the title of a LaTeX document, after the \begin{document} command but before the \maketitle command. The in-line R code would extract one or two pieces of information from an R data-frame created early in the R script I'm embedding in LaTeX.
I have a couple of Knitr chunks that create a data.frame from which I derive the information I want to put in the Title. I've tried placing these chunks between LaTeX's \begin{document} call and the \title code, like this:
\documentclass
[LaTex Preamble]
\begin{document}
[%% Knitr chunks that initialize an R data-frame]
\title \Sexpr{--a snippet of R code that extracts an element from the data-frame --}
\maketitle
... (rest of the LaTeX document)
and I've also tried putting the Knitr chunks in the preamble to the LaTeX code before \begin{document} statement.
But in Knitr seems to ignore code (other than initialization) that is placed ahead of the \maketitle call in LaTeX, so the in-line snippets included the title look like errors to Latex and it halts output.
I can't find any information in the Knitr documentation on including in-line code in the Title of a LaTeX document.
Any ideas?
OK: Found the solution thanks to the hint from #ben-bolker below. Ben uses the formatting of R chunks before output to an RNW file (in a 2-step Knitr process: latex -> rnw -> pdf) . But I'm compiling the LaTeX file to PDF in one-step without going to an RNW file from inside TeXShop (on Mac OSX). I found that I could get Ben's example to work using the RNW delimiters (<<>>=) and one-step compiling. But I couldn't mix the usual LaTeX chunk-delimiters (%%begin.rcode and %% end.rcode) and the RNW in-line statement hook (\Sexpr{}). The latter didn't work no matter how I fiddled with it. Eventually I found that the correct in-line hook for LaTeX is \\rinline{}.
It's not very clear in the Knitr documentation that this is the required format for LaTeX and I found it eventually mainly thanks to Ben's example. Best, Peter
Update 2 ... and then there's RTFM (or the 'cheat sheet' in this case): http://cran.r-project.org/web/packages/knitr/vignettes/knitr-refcard.pdf
Hmm. The following file works for me:
\documentclass{article}
<<echo=FALSE>>=
x <- 5
#
\title{The number is \Sexpr{x^2}}
\begin{document}
\maketitle
Some stuff
\end{document}
with knitr version 0.8 on Ubuntu 10.04, via knit2pdf("knitr_title.Rnw") ...
I would like to make an R code chunk (in Sweave) printed inside a framed box in the resulting pdf.
Is there an easy solution for doing that?
The short answer is that yes, there is an easy way. Just add the following lines, or something like them to the preamble of your Sweave document:
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em,
frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em,
frame=single}
This works because the appearance of code (and output) chunks is controlled by the definition of the Sinput and Soutput environments. These are both Verbatim environments as provided by the LaTeX package fancyvrb. (Click here for a 73 page pdf describing the numerous options that fancyvrb provides).
A quick look in the file Sweave.sty reveals the default definition of those two environments:
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
To change those definitions, just add \DefineVerbatimEnvironment statements of your own devising either: (a) at the end of the Sweave.sty file; or (b) at the start of your *.Snw document.
Finally, here's an example to show what this looks like in practice:
\documentclass[a4paper]{article}
\usepackage{Sweave}
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em,
frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em,
frame=single}
\title{Sweave with boxes}
\begin{document}
\maketitle
<<echo=FALSE>>=
options(width=60)
#
Here is an example of a code chunk followed by an output chunk,
both enclosed in boxes.
<<>>=
print(rnorm(99))
#
\end{document}
knitr, a successor of Sweave, by default outputs all echoed R code in boxes, and also formats it to the margins. Other nice features include syntax coloring and PGF integration.
Sweave code of average complexity needs only minor if any adaptions to run with knitr.