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Category Archives: howto
Exploring color palettes in R
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 data visualization, methods, population genetics
8 Comments
LaTeX hacks to save your life (and your co-authors')
In light of this recent study by Knauff and Nejasmic (2014) that makes a lot of presumptive leaps on the utility and effectiveness of in scientific writing, my case for the utility of for every equation, reference, table, figure, and … Continue reading
SpaceMix, and a brief history of Spatial Genetics
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 data visualization, isolation by distance, methods, population structure
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A population genetic R-evolution
Uphill, both ways, in the snow, without shoes … quite apt when thinking of the dark days, in the not too distant past, in which a separate input file was needed for each popgen analysis in order to use a … Continue reading
Posted in howto, methods, population genetics, R, software, Uncategorized
3 Comments
Linking gene expression and phenotype in an emerging model organism
Last week in his post “Transcriptomics in the wild (populations),” TME contributor Noah Snyder-Mackler focused on a recent paper by Alvarez et al. that reviews the last decade of transcriptomic research including the goal of linking gene expression and phenotype. Researchers today routinely collect transcriptomic data for non-model … Continue reading
Posted in genomics, howto, methods, Uncategorized
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Migration Circos plots in R
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 data visualization, methods
11 Comments
Geophylogeny plots in R for Dummies
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 data visualization, population structure
4 Comments
Admixture maps in R for Dummies
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 data visualization, population structure
14 Comments
Using GitHub with R and RStudio
A few weeks back, The Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading
Posted in bioinformatics, howto, R, software
29 Comments