Welcome to R: Building Phylogenetic Trees with ggtree

In this workshop you will learn how to work with phylogenetic trees programatically using R, particularly using the package ggtree

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Workshop overview

Day 1: 100% of what you need to know to make basic trees in R

• Reading in different phylogenetic tree file types

• Plotting trees

Day 2: Neatly associating trees with complementary data

• Using metadata to subset and highlight features of a tree

• Plot trees alongside heatmaps

Day 3: Incorporating trees with quantitative data

• Adding ancestral state reconstruction data to trees

• Comparing and visualizing different tree topologies

• Plotting trees with bar plots

Session files

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.

Running workshop code

There are a couple of ways to run this workshop.

Option 1 (local):

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.

Option 2 (cloud):

Click here to run a version of this workshop through your browser using binder

Many thanks to Wayne (@Fomightez) for putting this together!

Repo fork for binder version

Check out Wayne's bioinformatics portal containg other useful bioinformatics tools and pipelines here!

Parts of a tree

Here are some useful terms to know when working with trees. The ggtree() equivalents are highlighted in maroon.

Reductase gene metadata

The metadata used throughout the workshop for reference.

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If you liked this workshop, consider taking a look at my Biopython workshop!

Acknowledgements and references

Please follow me on twitter! @alexmcfarland_

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.