r - incorporate code listings from an external file in knitr/markdown -
i incorporate listings of code drawn external files in rmarkdown file. pretty (syntax highlighting, auto-indentation, etc.).
- the code not r code (otherwise use of existing tricks pretty-print r functions) - specifically, it's bugs , stan code.
- i'm not targeting latex/pdf output: otherwise use
listingspackage. - i'd able incorporate files without unwieldy external
cat firstpart.rmd codefile.rmd lastpart.rmd >wholefile.rmdsystem command, , without pre-processing step: this question suggests markdown processors multimarkdown , marked 2 have file inclusion syntax, think i'm stuck pandoc. - at present i'm using code chunks this
```{r jagsmodel, echo=false, results="markup", comment=""} cat(readlines("logist.bug"),sep="\n") ``` which works ok doesn't me syntax highlighting ...
here's 1 approach. need pygments installed (pip install pygments) , has able put (it should on it's own) "pygmentize somewhere on system. if don't have python or can't install module, answer not going answer you.
the following knitr chunks (all last 1 pure r) call pygmentize create html markup code. should possible modify https://github.com/hrbrmstr/knitrengines make more "automagical" that's not on short-term todo.
--- title: "lexers" output: html_document: css: code.css keep_md: true --- ```{r setup, include=false} knitr::opts_chunk$set(echo = true) ``` ### bugs ```{r bugs1, echo=false, results="asis"} tf <- tempfile(fileext=".html") system(sprintf("/usr/local/bin/pygmentize -o %s incl.bug", tf)) cat(readlines(tf), sep="\n") unlink(tf) ``` ### elixir ```{r elixir1, echo=false, results="asis"} tf <- tempfile(fileext=".html") system(sprintf("/usr/local/bin/pygmentize -o %s incl.ex", tf)) cat(readlines(tf), sep="\n") unlink(tf) ``` ### python ```{r py1, echo=false, results="asis"} tf <- tempfile(fileext=".html") system(sprintf("/usr/local/bin/pygmentize -o %s incl.py", tf)) cat(readlines(tf), sep="\n") unlink(tf) ``` ### plain ol' r ```{r} summary(mtcars) ``` that makes:
you can use pygments css file different scheme, what's in code.css:
<style> .gl .hll { background-color: #ffffcc } .highlight { background: #f8f8f8; } .highlight .c { color: #408080; font-style: italic } /* comment */ .highlight .err { border: 1px solid #ff0000 } /* error */ .highlight .k { color: #008000; font-weight: bold } /* keyword */ .highlight .o { color: #666666 } /* operator */ .highlight .cm { color: #408080; font-style: italic } /* comment.multiline */ .highlight .cp { color: #bc7a00 } /* comment.preproc */ .highlight .c1 { color: #408080; font-style: italic } /* comment.single */ .highlight .cs { color: #408080; font-style: italic } /* comment.special */ .highlight .gd { color: #a00000 } /* generic.deleted */ .highlight .ge { font-style: italic } /* generic.emph */ .highlight .gr { color: #ff0000 } /* generic.error */ .highlight .gh { color: #000080; font-weight: bold } /* generic.heading */ .highlight .gi { color: #00a000 } /* generic.inserted */ .highlight .go { color: #808080 } /* generic.output */ .highlight .gp { color: #000080; font-weight: bold } /* generic.prompt */ .highlight .gs { font-weight: bold } /* generic.strong */ .highlight .gu { color: #800080; font-weight: bold } /* generic.subheading */ .highlight .gt { color: #0040d0 } /* generic.traceback */ .highlight .kc { color: #008000; font-weight: bold } /* keyword.constant */ .highlight .kd { color: #008000; font-weight: bold } /* keyword.declaration */ .highlight .kn { color: #008000; font-weight: bold } /* keyword.namespace */ .highlight .kp { color: #008000 } /* keyword.pseudo */ .highlight .kr { color: #008000; font-weight: bold } /* keyword.reserved */ .highlight .kt { color: #b00040 } /* keyword.type */ .highlight .m { color: #666666 } /* literal.number */ .highlight .s { color: #ba2121 } /* literal.string */ .highlight .na { color: #7d9029 } /* name.attribute */ .highlight .nb { color: #008000 } /* name.builtin */ .highlight .nc { color: #0000ff; font-weight: bold } /* name.class */ .highlight .no { color: #880000 } /* name.constant */ .highlight .nd { color: #aa22ff } /* name.decorator */ .highlight .ni { color: #999999; font-weight: bold } /* name.entity */ .highlight .ne { color: #d2413a; font-weight: bold } /* name.exception */ .highlight .nf { color: #0000ff } /* name.function */ .highlight .nl { color: #a0a000 } /* name.label */ .highlight .nn { color: #0000ff; font-weight: bold } /* name.namespace */ .highlight .nt { color: #008000; font-weight: bold } /* name.tag */ .highlight .nv { color: #19177c } /* name.variable */ .highlight .ow { color: #aa22ff; font-weight: bold } /* operator.word */ .highlight .w { color: #bbbbbb } /* text.whitespace */ .highlight .mf { color: #666666 } /* literal.number.float */ .highlight .mh { color: #666666 } /* literal.number.hex */ .highlight .mi { color: #666666 } /* literal.number.integer */ .highlight .mo { color: #666666 } /* literal.number.oct */ .highlight .sb { color: #ba2121 } /* literal.string.backtick */ .highlight .sc { color: #ba2121 } /* literal.string.char */ .highlight .sd { color: #ba2121; font-style: italic } /* literal.string.doc */ .highlight .s2 { color: #ba2121 } /* literal.string.double */ .highlight .se { color: #bb6622; font-weight: bold } /* literal.string.escape */ .highlight .sh { color: #ba2121 } /* literal.string.heredoc */ .highlight .si { color: #bb6688; font-weight: bold } /* literal.string.interpol */ .highlight .sx { color: #008000 } /* literal.string.other */ .highlight .sr { color: #bb6688 } /* literal.string.regex */ .highlight .s1 { color: #ba2121 } /* literal.string.single */ .highlight .ss { color: #19177c } /* literal.string.symbol */ .highlight .bp { color: #008000 } /* name.builtin.pseudo */ .highlight .vc { color: #19177c } /* name.variable.class */ .highlight .vg { color: #19177c } /* name.variable.global */ .highlight .vi { color: #19177c } /* name.variable.instance */ .highlight .il { color: #666666 } /* literal.number.integer.long */ </style> update
if you're willing put code (that won't executed formatted) inline, made update aforementioned knitrengines package lets this:
--- title: "pygtest" output: html_document --- ```{r setup, include=false} knitr::opts_chunk$set(echo = true) library(knitrengines) ``` ```{pygments test, pyg.ext="py", pyg.sty="github"} import something.please print("hello, world!") ``` ```{pygments test2, pyg.ext="go", pyg.sty="github"} package main import "fmt" func main() { s := make([]string, 3) fmt.println("emp:", s) s[0] = "a" s[1] = "b" s[2] = "c" twod := make([][]int, 3) := 0; < 3; i++ { innerlen := + 1 twod[i] = make([]int, innerlen) j := 0; j < innerlen; j++ { twod[i][j] = + j } } fmt.println("2d: ", twod) } ``` ```{pygments test3, pyg.ext="ex", pyg.sty="github"} defmodule math def sum(a, b) + b end end io.puts "the answer #{ math.sum(4,3) }" ``` and produces this:
i can make use different styles per code block, barely had cycles crank out. shouldn't work tho.
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