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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

tree with heatmaps

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() equiavalents are highlighted in maroon.

different terms used to describe a tree

Reductase gene metadata

The metadata used throughout the workshop for reference.

metadata for reductase genes

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.