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R Bioinformatics Cookbook

You're reading from   R Bioinformatics Cookbook Utilize R packages for bioinformatics, genomics, data science, and machine learning

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Product type Paperback
Published in Oct 2023
Publisher Packt
ISBN-13 9781837634279
Length 396 pages
Edition 2nd Edition
Languages
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Author (1):
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Dan MacLean Dan MacLean
Author Profile Icon Dan MacLean
Dan MacLean
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Toc

Table of Contents (16) Chapters Close

Preface 1. Chapter 1: Setting Up Your R Bioinformatics Working Environment 2. Chapter 2: Loading, Tidying, and Cleaning Data in the tidyverse FREE CHAPTER 3. Chapter 3: ggplot2 and Extensions for Publication Quality Plots 4. Chapter 4: Using Quarto to Make Data-Rich Reports, Presentations, and Websites 5. Chapter 5: Easily Performing Statistical Tests Using Linear Models 6. Chapter 6: Performing Quantitative RNA-seq 7. Chapter 7: Finding Genetic Variants with HTS Data 8. Chapter 8: Searching Gene and Protein Sequences for Domains and Motifs 9. Chapter 9: Phylogenetic Analysis and Visualization 10. Chapter 10: Analyzing Gene Annotations 11. Chapter 11: Machine Learning with mlr3 12. Chapter 12: Functional Programming with purrr and base R 13. Chapter 13: Turbo-Charging Development in R with ChatGPT 14. Index 15. Other Books You May Enjoy

Visualizing trees of many genes quickly with ggtree

Once you have computed a tree, the first thing you will want to do with it is take a look. That’s possible in many programs, but R has an extremely powerful, flexible, and fast system in the form of the ggtree package. In this recipe, we’ll learn how to get into ggtree and re-layout, highlight, and annotate tree images in just a few commands.

Getting ready

You’ll need the ggplot2, ggtree, and ape packages. You’ll also require the itol.nwk file from the rbioinfcookbook package. The file is a Newick tree of 191 species from the Interactive Tree of Life online tool’s public dataset. At the time of writing, there is an issue with an upstream dependency that causes this code to fail, though it is correct. We hope this will have gone away by the time you read this. If it hasn’t, a workaround is to install the source version of ggtree from Biocmanager, like this:

BiocManager::install(&quot...
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