Articles by Stewart MacArthur

R tip: Maximum screen width

April 19, 2010 | Stewart MacArthur

R can be annoying in that even if you stretch your terminal or R GUI session to a whole screen width it will still only show 80 characters width. This can make wide tables really hard to read. options(width=150)Use the options command width to set... [Read more...]

R: heatmaps with gplots

April 8, 2010 | Stewart MacArthur

I use heatmaps quite a lot for visualizing data, microarrays of course but also DNA motif enrichment, base composition and other things. I particular like the heatmap.2 function of the gplots package. It has a couple of defaults that are a little ugly ... [Read more...]

Sweave in TeXShop

December 21, 2009 | Stewart MacArthur

I love using TeXShop for GUI editing of LaTeX and particularly Sweave documents, but it is a pain not being able to get it to automatically generate the pdf output. Luckily I found this post which explains how to add a Sweave engine.Basically, make a f... [Read more...]

R tip: Extracting median from survfit object

November 17, 2009 | Stewart MacArthur

A colleague wanted to extract the median value from a survival analysis object, which turned out to be a pain as the value is not stored in the object, but calculated on the fly by a print method. __ library(survival)__ fit __ survfit(fit)Call: survfit(formula = fit)records n.max ... [Read more...]

RSPerl : Using R from within Perl

October 23, 2009 | Stewart MacArthur

Some things I write in perl some in R, sometime I use perl to write R and run R. One thing that I find very useful is the functionality of RSPerl which enables you to call R functions from within perl and on perl variables. It can also call perl ... [Read more...]


July 27, 2009 | Stewart MacArthur

I use R and Bioconductor for most of my work. I am also increasingly replacing things I would have done before in Perl with R. One such example of this is the Bioconductor module biomaRt.As the name suggest it allows for access to BioMart via R. BioMart is a ... [Read more...]

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