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r functions: knitr wrapper

in programming on 13 July 2013

Summary

Thought i'd share the wrapper function i use to knit files using the excellent knitr package in R. This allows easy creation of an html page that integrates commentary, R code, and the resulting plots (which are base64 encoded, so the html file is fully portable).

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Thought i'd share the wrapper function i use to knit files using the excellent knitr package in R. This allows easy creation of an html page that integrates commentary, R code, and the resulting plots (which are base64 encoded, so the html file is fully portable). The code is pretty readable and commented, so i won't explain each part. Enjoy!

download knitr.compile.toHTML.R

R / S+
  1. # biafra ahanonu
  2. # updated: 2013.07.13
  3. # knitr wrapper function
  4. # ________________________________________________________
  5. # load libraries
  6. require(knitr)
  7. require(markdown)
  8. # ________________________________________________________
  9. flipExt <- function(input,ext){
  10.         # loop over and process files in the list
  11.         return(paste(c(head(unlist(strsplit(input,'\\.')),-1),ext),sep=".",collapse="."))
  12. }
  13. gsubFile <- function(file,pattern,replacement){
  14.         # substitute multiple patterns in a file, create temporary file to process
  15.         newFile = paste(file,'.tmp.Rmd',sep="")
  16.         for (i in 1:length(pattern)){
  17.                 fileContents <- readLines(file)
  18.                 modifiedContents <- gsub(pattern[i],replacement[i], fileContents)
  19.                 cat(modifiedContents, file=newFile, sep="\n")
  20.         }
  21.         return(newFile)
  22. }
  23. knitFileToHTML <-function(rmdFileList=c('TheFile.Rmd'), newDir="./"){
  24.         #knit files in newDir together, defaults to current directory
  25.         # move to folder with file
  26.         oldDir = getwd()
  27.         # cd to new directory
  28.         setwd(newDir)
  29.  
  30.         # knit that file!
  31.         for (rmdFile in rmdFileList){
  32.                 # so you can indent R blocks, also suppress warnings/error messages
  33.                 newRmdFile = gsubFile(rmdFile,c("\t```\\{r\\}","\t```"),c("```\\{r warning=FALSE, error=FALSE\\}","```"))
  34.                 # get html/md filenames
  35.                 mdFile = flipExt(newRmdFile,'md')
  36.                 htmlFile = flipExt(newRmdFile,'html')
  37.                 # knit to markdown
  38.                 knit(newRmdFile)
  39.  
  40.                 # extra html to add for style (prevent code/images from overflowing horizontal page boundaries)
  41.                 extraHtml = '<style>body{width:80%;margin-left:auto;margin-right:auto;}img,pre,code{white-space:pre-wrap;max-width:100%;margin-left:auto;margin-right:auto;}pre{border: 0px solid #ccc;}code.r{border: 1px solid #ccc;}div#toc{-moz-column-count: 4;-webkit-column-count: 4;-moz-column-gap: 1em;-webkit-column-gap: 1em;-moz-column-rule: 1px solid black;-webkit-column-rule: 1px solid black;}li{display:block;}</style>'
  42.                 # append extra html to markdown file
  43.                 write(extraHtml,file=mdFile,append=TRUE)
  44.  
  45.                 # convert to html
  46.                 markdownToHTML(file=mdFile,output=htmlFile,options=c('toc',"use_xhtml","smartypants","base64_images","mathjax","highlight_code"))
  47.  
  48.                 # remove md and temp Rmd file
  49.                 unlink(c(newRmdFile,mdFile))
  50.         }
  51.  
  52.         # return to old directory
  53.         setwd(oldDir)
  54. }
  55.  
  56. # run the script
  57. knitFileToHTML(rmdFileList=c('TheFile.Rmd'), newDir="./")

-biafra
bahanonu [at] alum.mit.edu

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