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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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syntax highlighting in vignettes using knitr #98

Closed joey711 closed 12 years ago

joey711 commented 12 years ago

The knitr package appears to be a good alternative to Sweave for building Rnw files. It has extra options, supports caching, syntax highlighting, and several other graphics/display options that make better-looking documents.

Check out its official web documentation:

http://yihui.name/knitr/

@yihui is also a contributor to roxygen and animation. Checkout the GitHub page for knitr here:

https://github.com/yihui/knitr

joey711 commented 12 years ago

This is trivial to do using the latest build of RStudio. Just switch the "Sweave" options from "Sweave" to "knitr" for weaving the latex. However, the way in which you've written the analysis vignette is currently causing some problems with the knitr-flavored weaving. Should probably consider re-writing in some fashion or another, maybe getting away from "manual" ggsave for plots and keeping everything more integrated. phyloseq_basics vignette enjoys the knitr-flavored syntax highlighting now, though.

fb7e1c6560248a069f3af0a8447088910e755c26

This issue can be considered closed once the analysis vignette is updated to work with knitr as well...

joey711 commented 12 years ago

Done. Syntax highlighting and reasonable formatting now in both vignettes.

4df90cc42249d9a650b051463f6f5bfe36dbc604