January 13, 2011

(This article was first published on rforcancer, and kindly contributed to R-bloggers)

I have just remembered a package called ‘prettyR’ that pretty much does what it says. It makes R code more readable.. so an example from my forthcoming genomeplot package (see forthcoming blog entry):


## this function integrates 3 steps to creating a genome plot
## 1 query bioMart to get a GFF like data-frame from ensembl
## 2 add new elements to the gff to make it plot with ggplot2
## 3 plot it with ggplot2
## the reason to split it like this is so that basic users may use this simple function
## and advanced users can try custom queries or altered plotting themes with the sep functions
gnmplot= function(filters='hgnc', values='MAF', species='human')
require(biomaRt); require(ggplot2)
gff= getGFF(filters=filters, values=values, species=species)

which I think you will agree.. is quite nice. So in future I’ll be using this for all R-code on the website.


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