Tag Archives: data visualization

Exploring color palettes in R

Posted on 12 Mar, 2015 by Arun Sethuraman

How often have you had to squint at figures with unpleasant color palettes in a manuscript online or in print, and ultimately given up on distinguishing between fifty (or maybe just around 30) shades of gray? I found the RColorBrewer … Continue reading →

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , , | 8 Comments

Phonemes and Genomes

Posted on 5 Feb, 2015 by Arun Sethuraman

Human phonemes and genomes are thought to have evolved hand-in-glove out of Africa. Several recent studies have attempted to capture a picture of this global variation in languages and peoples, often supporting (and rejecting) a serial founder model (eg. see … Continue reading →

Posted in bioinformatics, evolution, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

SpaceMix, and a brief history of Spatial Genetics

Posted on 15 Jan, 2015 by Arun Sethuraman

Incorporating spatial data to inform studies of the population demography of a species has a long history of interest. From inferring geographical clines in Principal Components Analyses (Menozzi et al. 1978), using location data as “informative priors” during model-based estimation … Continue reading →

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | Leave a comment

Migration Circos plots in R

Posted on 11 Dec, 2014 by Arun Sethuraman

We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading →

Posted in bioinformatics, genomics, howto, R, software | Tagged , | 11 Comments

Geophylogeny plots in R for Dummies

Posted on 27 Nov, 2014 by Arun Sethuraman

Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with … Continue reading →

Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE | Tagged , | 4 Comments

Admixture maps in R for Dummies

Posted on 13 Nov, 2014 by Arun Sethuraman

Before we get started, I’d like to point everyone to an excellent tutorial here by Kim Gilbert on making maps in R. I have been grappling with overlaying admixture plots, and migration routes on top of maps recently, and thought I’d put … Continue reading →

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , | 14 Comments

Show us your molecular ecology!

Posted on 11 Feb, 2013 by Jeremy Yoder

Anyone who’s hung around the blogosphere long enough is familiar with the “View From Your Window” feature at Andrew Sullivan’s blog, in which readers send in photos of, well, exactly what it says on the tin. The result is a … Continue reading →

Posted in community, Molecular Ecology views | Tagged , | 7 Comments

What we're reading

Posted on 7 Dec, 2012 by Jeremy Yoder

As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen time. In the journals Desai, M.M., Walczak, A.M. & Fisher, D.S. 2012. Genetic diversity and the structure of genealogies in rapidly adapting … Continue reading →

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