Tag Archives: data visualization

Simple tools for mastering color in scientific figures

Posted on 23 Apr, 2020 by Patrícia Chrzanová Pečnerová

Call me a procrastinator but I strongly believe that spending time to select a good color scheme can work miracles with a plot, paper, or presentation. In science, it’s generally not expected that you invest time into a thought process … Continue reading →

Posted in howto, methods, Science Communication, science publishing | Tagged , , , , , , , , , , | 1 Comment

On (mis)interpreting STRUCTURE/ADMIXTURE results

Posted on 5 Aug, 2016 by Arun Sethuraman

STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading →

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , , , | 1 Comment

The Truth

Posted on 17 Mar, 2016 by Arun Sethuraman

Spoiler Alert: I’ve taken plenty of care to try and not spill the beans on any plotlines, but you have been forewarned that there may be some aspects of the science that’s discussed on the show that I attempt to … Continue reading →

Posted in genomics, next generation sequencing, population genetics, TV shows | Tagged , , , , , | Leave a comment

Geographical Heat Maps in R

Posted on 3 Mar, 2016 by Arun Sethuraman

I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading →

Posted in bioinformatics, howto, R, software | Tagged , | 2 Comments

2D Posterior Density Plots in R

Posted on 6 Nov, 2015 by Arun Sethuraman

I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading →

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 1 Comment

PCA of multilocus genotypes in R

Posted on 30 Jul, 2015 by Arun Sethuraman

An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading →

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 6 Comments

IBE/IBD Contour plots in R

Posted on 18 Jun, 2015 by Arun Sethuraman

Rob’s post from yesterday motivated me to find an alternate way of visualizing correlations between matrices of geographical or ecological data, and genetic data. I have seen plenty of Mantel, or partial Mantel tests of correlation, as well as plots … Continue reading →

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 5 Comments

Procrustes Analyses in R

Posted on 23 Apr, 2015 by Arun Sethuraman

Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geographical and genetic distributions of species, following the lead of Wang et … Continue reading →

Posted in genomics, howto, population genetics, R, software | Tagged , , , | 3 Comments

Visualizing Linkage Disequilibrium in R

Posted on 9 Apr, 2015 by Arun Sethuraman

Patterns of Linkage Disequilibrium (LD) across a genome has multiple implications for a population’s ancestral demography. For instance, population bottlenecks predictably result in increased LD, LD between SNP’s in loci under natural selection affect each others rates of adaptive evolution, selfing/inbreeding populations … Continue reading →

Posted in bioinformatics, howto, population genetics, R | Tagged , , | 1 Comment

F-statistics Manhattan Plots in R

Posted on 26 Mar, 2015 by Arun Sethuraman

Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading →

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 4 Comments