04 November 2013

knitr and Sweave

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Monday notes

Sara reported on EcoGen meeting in KC

  • iPath may be useful tool for identifying genes in metabolic pathways


slideshare on python

NG wrote an R shell script to generate html file from Rmd file. Modified script to generate a pdf from markdown file using system call to pandoc.

Information on command-line call to knitr here. The answer is

Rscript -e "library(knitr); knit('myfile.Rmd')"

In comments, Yihui includes link to an Rscript that doe Rmd->html or Rnw->pdf from command line, knit file.Rmd. Elegant script - nice example for using R as a program with command-line arguments! Added script to /usr/local/bin so globally available.

Info on how you what R CMD Sweave does


Consider using TrinotateWeb with or in place of shiny for web documentation of assembly

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