#LyX 2.0 created this file. For more info see http://www.lyx.org/ \lyxformat 413 \begin_document \begin_header \textclass article \use_default_options true \begin_modules knitr \end_modules \maintain_unincluded_children false \language english \language_package none \inputencoding default \fontencoding global \font_roman palatino \font_sans default \font_typewriter default \font_default_family default \use_non_tex_fonts false \font_sc true \font_osf false \font_sf_scale 100 \font_tt_scale 100 \graphics default \default_output_format default \output_sync 0 \bibtex_command default \index_command default \paperfontsize default \spacing single \use_hyperref true \pdf_bookmarks true \pdf_bookmarksnumbered true \pdf_bookmarksopen true \pdf_bookmarksopenlevel 2 \pdf_breaklinks false \pdf_pdfborder false \pdf_colorlinks false \pdf_backref false \pdf_pdfusetitle true \pdf_quoted_options "pdfstartview={XYZ null null 1}" \papersize default \use_geometry true \use_amsmath 1 \use_esint 1 \use_mhchem 1 \use_mathdots 1 \cite_engine basic \use_bibtopic false \use_indices false \paperorientation portrait \suppress_date false \use_refstyle 1 \index Index \shortcut idx \color #008000 \end_index \leftmargin 2.5cm \topmargin 2.5cm \rightmargin 2.5cm \bottommargin 2.5cm \secnumdepth 3 \tocdepth 3 \paragraph_separation indent \paragraph_indentation default \quotes_language english \papercolumns 1 \papersides 1 \paperpagestyle default \listings_params "language=R" \tracking_changes false \output_changes false \html_math_output 0 \html_css_as_file 0 \html_be_strict false \end_header \begin_body \begin_layout Standard \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout library(knitr) \end_layout \begin_layout Plain Layout opts_chunk$set(fig.path = 'figure/listings-') \end_layout \begin_layout Plain Layout options(formatR.arrow = TRUE) \end_layout \begin_layout Plain Layout render_listings() \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \begin_layout Title Using listings with knitr \end_layout \begin_layout Author Yihui Xie \end_layout \begin_layout Standard To use the \series bold listings \series default package with \series bold knitr \series default , all you need to do is to call a function in your first setup chunk (that chunk should be hidden from the output with \family typewriter include=FALSE \family default and should not be cached): \end_layout \begin_layout Standard \begin_inset ERT status open \begin_layout Plain Layout % I just want to echo the 2nd line \end_layout \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \begin_layout Standard This function modifies the output hooks and header information so that the output is written in \series bold listings \series default environments, which are kindly provided by Frank Harrell and can be found in \begin_inset Flex URL status collapsed \begin_layout Plain Layout https://github.com/yihui/knitr/blob/master/inst/misc/Sweavel.sty \end_layout \end_inset . Of course you have to install the \series bold listings \series default package if your LaTeX toolset does not include this package. \end_layout \begin_layout Standard Now we can see how the results look like with our new settings: \end_layout \begin_layout Standard \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout set.seed(1121) # for reproducibility \end_layout \begin_layout Plain Layout options(width=85) \end_layout \begin_layout Plain Layout x=rnorm(20) \end_layout \begin_layout Plain Layout x \end_layout \begin_layout Plain Layout mean(x) \end_layout \begin_layout Plain Layout sqrt(-1) # this will give you a warning message \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \begin_layout Standard Another chunk: \end_layout \begin_layout Standard \begin_inset ERT status open \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout hook_rgl = function(before, options, envir) { \end_layout \begin_layout Plain Layout ## after a chunk has been evaluated \end_layout \begin_layout Plain Layout if (before || !require('rgl') || rgl.cur() == 0) return() # no active device \end_layout \begin_layout Plain Layout name = paste(valid_prefix(options$fig.path), options$label, sep = '') \end_layout \begin_layout Plain Layout par3d(windowRect = 100 + options$dpi * c(0, 0, options$width, options$height )) \end_layout \begin_layout Plain Layout Sys.sleep(.05) # need time to respond to window size change \end_layout \begin_layout Plain Layout \end_layout \begin_layout Plain Layout fmt = opts_knit$get('out.format') \end_layout \begin_layout Plain Layout if (fmt %in% c('html', 'markdown', 'gfm', 'jekyll')) options$dev = 'png' \end_layout \begin_layout Plain Layout \end_layout \begin_layout Plain Layout ## support 3 formats: eps, pdf and png (default) \end_layout \begin_layout Plain Layout switch(options$dev, \end_layout \begin_layout Plain Layout postscript = rgl.postscript(paste(name, '.eps', sep = ''), fmt = 'eps'), \end_layout \begin_layout Plain Layout pdf = rgl.postscript(paste(name, '.pdf', sep = ''), fmt = 'pdf'), \end_layout \begin_layout Plain Layout rgl.snapshot(paste(name, '.png', sep = ''), fmt = 'png')) \end_layout \begin_layout Plain Layout \end_layout \begin_layout Plain Layout if (fmt == 'html') return(.plot.hook.html(c(name, 'png'), options)) \end_layout \begin_layout Plain Layout if (fmt %in% c('markdown', 'gfm', 'jekyll')) \end_layout \begin_layout Plain Layout return(.plot.hook.markdown(c(name, 'png'), options)) \end_layout \begin_layout Plain Layout \end_layout \begin_layout Plain Layout paste(ifelse(options$align == 'center', ' \backslash \backslash centering{}', ''), ' \backslash \backslash includegraphics[', \end_layout \begin_layout Plain Layout sprintf('width=%s', options$out.width), ']{', name, '} \backslash n', sep = '') \end_layout \begin_layout Plain Layout } \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \begin_layout Standard Well, we can do crazier things with \series bold knitr \series default . Here we use the \family typewriter fig.cap \family default option to write plots into the \family typewriter figure \family default environment automatically, and the caption is generated from data dynamically (see Figure \begin_inset ERT status collapsed \begin_layout Plain Layout \backslash ref{fig:boxplot-ex} \end_layout \end_inset ): \end_layout \begin_layout Standard \begin_inset ERT status open \begin_layout Plain Layout % set an option first \end_layout \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout opts_knit$set(eval.after = 'fig.cap') # evaluate fig.cap after the chunk \end_layout \begin_layout Plain Layout \end_layout \begin_layout Plain Layout <>= \end_layout \begin_layout Plain Layout par(mar=c(4,4,.1,.1)) \end_layout \begin_layout Plain Layout boxplot(x, horizontal=TRUE) \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \begin_layout Standard As we know, \family typewriter figure \family default is a float environment, so it has floated away from the R code to the top of this page. This should not be surprising to LaTeX users. \end_layout \begin_layout Standard You should be able to compile the TeX document and get a PDF file like this one: \begin_inset Flex URL status collapsed \begin_layout Plain Layout https://github.com/yihui/knitr/releases/download/doc/knitr-listings.pdf \end_layout \end_inset . For more information about out hooks, see \begin_inset Flex URL status collapsed \begin_layout Plain Layout https://yihui.org/knitr/hooks/ \end_layout \end_inset . \end_layout \end_body \end_document