In this workshop you will learn how to work with phylogenetic trees programatically using R, particularly using the package ggtree
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Reading in different phylogenetic tree file types
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Plotting trees
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Using metadata to subset and highlight features of a tree
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Plot trees alongside heatmaps
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Adding ancestral state reconstruction data to trees
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Comparing and visualizing different tree topologies
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Plotting trees with bar plots
There are three R Markdown (.rmd) files for each day of the workshop.
There are also three R Markdown files containing the answers to each of the day's exercises.
Each day has a knitted R Markdown .html file that can be used as a reference. Exercise code is left unrun.
There are a couple of ways to run this workshop.
Click on the green Code button and choose Download Zip, unzip the folder on your computer, open the appropriate R Markdown file.
Please make sure that you have all packages installed! The install.packages()
command for each package is included in the first code cell of each R Markdown file.
Click the following badge to run a version of this workshop through your browser using MyBinder:
Many thanks to Wayne (@Fomightez) for putting this together!
Here are some useful terms to know when working with trees. The ggtree()
equiavalents are highlighted in maroon.
The metadata used throughout the workshop for reference.
Northwestern University Information Technology Research Computing Services
Special thanks to Colby Witherup Wood for their assistance
Many thanks to Wayne Decatur for adapting the code for binder
G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96.
Paradis E, Schliep K (2019). “ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.” Bioinformatics, 35, 526-528.
G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194.
G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi: 10.1111/2041-210X.12628.
Clarifying Attribution: I, Wayne (fomightez@GitHub), am not involved in this workshop at all. The person who authored the featured content is Alex McFarland. See Alex's materials, such as the original repo for the workshop. I simply set up this fork of the repository to make the software useable in RStudio without installation headaches and in a full-featured, browser-based computational environment.
(Related to this, upon session launch, the most current current Rmarkdown files are retrieved from Alex's source repo so that anyone using this via MyBinder.org has the most current content available.)