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Category Archives: R
Phylogenetic trees in R using ggtree
Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has … Continue reading
Posted in bioinformatics, howto, phylogenetics, R
Tagged ggtree, phylogenetics, phylogenomics, R
2 Comments
Video Tutorial: editing R plots in Adobe Illustrator
Adobe Illustrator is a powerful tool for creating and editing figures; unfortunately, it’s also really intimidating. So today at The Molecular Ecologist we’re trying something a little different: a screen-capture video tutorial about using Adobe Illustrator to enhance and edit plots … Continue reading
Posted in howto, R
Tagged Adobe, Figures, how to, Illustrator, Plots, R, Screen Capture, Tutorial, Video
3 Comments
Making Maps in R, volume 2: ggplots
The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the … Continue reading
Geographical Heat Maps in R
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
Quick and dirty tree building in R
One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading
Posted in howto, methods, phylogenetics, R, software
Tagged ape, distance matrices, maximum likelihood, nucleotide evolution, parsimony, phangorn, phylogenetics, R
3 Comments
2D Posterior Density Plots in R
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 data visualization, genomics, population genetics, R
1 Comment
Models matter when linking genetic diversity to niche model predictions
Ecological niche models and the methods to create them continue to evolve. These techniques provide a tidy way to relate the distributions of taxa to environmental variables from the present, past, or future. Oh, and they are pretty too: Those pretty … Continue reading
PCA of multilocus genotypes in R
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 data visualization, Homo sapiens, R
6 Comments