It all started when I wanted to have significant p-values shown on the terminal colored in red. The R terminal is capable of showing colors, simple formatting (like italics or bold) and Unicode characters, thanks to the actual terminal that does the job of displaying R output – whether it is ... [Read more...]

Quick and dirty Rmarkdown syntax highlighting for vim, when you don’t have time install bundles, plugins or dependencies: go to this github repository, download the file rmd.vim from the syntax/ directory and copy it to ~/.vim/syntax/. This should work in 99,99% of the cases. [Read more...]

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If you make the error which I did, you will try to use the data (say, “pckgdata”) from another package (say, “pckg”) naively like this: This will result in an error: Here is the solution (thanks to the comments from stackexchange: [Read more...]

Unfortunately, you need both: R-devel (development version of R) if you want to submit your packages to CRAN, and regular R for your research (you don’t want the unstable release for that). Fortunately, installing R-devel in parallel is less trouble than one might think. Say, we want to install ... [Read more...]

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So I have finally switched to knitr for doing my vignettes. The result is satisfactory, but the process was not entirely painless. The command to run instead of “R CMD Sweave foo.Rnw” is Rscript -e 'rmarkdown::render("foo.rmd")' I think that the concept of writing a package ... [Read more...]

Pandoc + markdown seem to be a great way of documenting my work. Markdown syntax is very simple and allows to add basic formatting and figures to an otherwise simple text document, without obfuscating the actual text. Then I simply compile the document using the pandoc command: There are some more ... [Read more...]

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Umph, that was a tough one. I spent ages figuring out how to do it correctly. I have a server running apache (on port 80) and shiny on port (say) 11111. Shiny has its own document root, and within this root, we have a shiny app, say, “example”. So to view this ... [Read more...]

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Say your function in sapply returns a matrix with a variable number of rows. For example sapply is too stupid to see the pattern here (or maybe I don’t know how to cast the return value into an appropriate shape…). The result of the above is a list: [[1]] [,1] [,2] [,3] [1,] 1 1 […] [Read more...]

The biomaRt package allows to query the gigantic ensembl data base directly from R. Since it happens only once in a while, I find myself reading the biomaRt vignette every time I’m using it. Here are the crucial points for the most common application. The data frames f and ... [Read more...]

There are many options to do pathway analysis with R and BioConductor. First, it is useful to get the KEGG pathways: Of course, “hsa” stands for Homo sapiens, “mmu” would stand for Mus musuculus etc. Incidentally, we can immediately make an analysis using gage. However, gage is tricky; note that ... [Read more...]