Colouring in country maps

If there’s one thing I love more than a good tree it’s a good map. (And how wonderful it is when they combine!) In genomic epidemiology, maps are often super important for visualising where bacterial genomic data has come from and how bugs are moving about.

Sometimes I think this is just me being a map-o-phile, but when we didn’t include a map in our recent paper on the dissemination of Shigella sonnei, the maps ended up being created anyway by the authors of two commentary articles! (Commentaries here and here.)

So, I often find I need to indicate on a global map which countries we have sampled in a study. Here are two ways to do it:

(1) GeoChart Map Generator

This is a web tool where you just click on the name of the countries you want to colour and they are filled in on the map. The advantage is it’s quick and easy, and will produce an image good enough to take a screenshot for insertion into a PowerPoint or web page. Disadvantage is the resolution isn’t really good enough for printing out and definitely not high enough resolution for a figure in a paper.

Here’s an example:


Similar apps are available on other sites, including

(2) Edit a SVG map in Adobe Illustrator or a similar graphics editor. You can download suitable maps from Wikimedia Commons –

This will give you a publication-quality figure, which you can save straight to PDF. To select the right countries to colour in, you’ll need to know where they are on the map (!). It can be handy to use one of the web tools first to help locate all the countries if your geography isn’t great.

Here’s an example, showing the countries covered in the Shigella sonnei study:


For some ideas on combining trees with maps, ie phylogeography, see this site for building tree maps for BEAST analyses using SPREAD, or try GenGIS.


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