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Maps in R: choropleth maps

R blog By January 24, 2013 Tags: , , 10 Comments

This is the third article of the Maps in R series. After having shown how to draw a map without placing data on it and how to plot point data on a map, in this installment the creation of a choropleth map will be presented.

A choropleth map is a thematic map featuring regions colored or shaded according to the value assumed by the variable of interest in that particular region.

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Maps in R: Introduction - Drawing the map of Europe

R blog By December 19, 2012 Tags: , , 18 Comments

This post is a brief follow-up to a question that appeared some time ago on the “The R Project for Statistical Computing” LinkedIn group, which I’m reporting here:

How can I draw a map of MODERN Europe?

Hi, I'm trying to draw a map of modern Europe but I've found only maps of twenty years ago, with Yugoslavia and Czechoslovakia still united!!!
Does anyone know where I can get a more recent map to be employed with packages such as 'sp' or 'maps'?
Thank you very much!

Two different solutions to the above question will be provided here, using two different R packages.

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Genome annotation with NCBI2R

R blog By November 19, 2012 Tags: , , No Comments

It's very convenient manage data with R: you can import your dataset, you could find many packages which respond to your needs, then you could plot your results.
However it could be very bothersome retrieve the data from online databases. You need to use the specific API and maybe write your scripts using a new programming language, then you have to convert your data in a table format and finally import them with R.

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Divide or Mix. Flexible Approaches to Data Analysis

R blog By September 19, 2012 Tags: , , No Comments

A very interesting paradigm in data analysis comes from the necessity to model data where it is difficult to think of a single global function to be capable to represent adequately the data.

We could see a spectrum of models going from the global statistical model, with a single function and associated probability distribution, to the decision tree fitting a set of constants at each leaf of the tree.

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GenABEL: an annoying error after the import of PLINK data format

R blog By July 12, 2012 Tags: , No Comments

In the previous post we saw how much convenient could be GenABEL in the management of genotypic/phenotypic data.
We introduced the import of genotypic data from an Illumina format file:
> convert.snp.illumina(inf = "gen.illu", out = "gen.raw", strand = "file")
but what happens if you're analysing your data with PLINK, the open source toolset for GWAS?

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