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R Bioinformatics Cookbook - Second Edition

You're reading from R Bioinformatics Cookbook - Second Edition

Product type Book

Published in Oct 2023

Publisher Packt

ISBN-13 9781837634279

Pages 396 pages

Edition 2nd Edition

Languages

Concepts

Author (1):

Dan MacLean

Table of Contents (16) Chapters

Preface

1. Chapter 1: Setting Up Your R Bioinformatics Working Environment

2. Chapter 2: Loading, Tidying, and Cleaning Data in the tidyverse

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

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15. Other Books You May Enjoy

Making interactive plots with plotly

Interactive plots are great tools for data exploration, allowing users to explore interactively large datasets to gain insights and identify patterns in data. They are useful for programmers wishing to create dashboards for visualizing real-time data and help with interactive presentations that can communicate complex data relationships in an engaging manner. plotly is a data visualization library for creating interactive plots in Python, R, and JavaScript. It provides a high-level interface for drawing attractive and informative statistical graphics, and the ggplotly package in R allows you to convert static ggplot2 visualizations to interactive plots through a high-level interface. In this recipe, we’ll create a fairly involved ggplot2 visualization of mutation sites on a genome and then convert it to plotly to get a great first-level interaction layer.

Getting ready

We’ll need the ggplot2, plotly, and rbioinfcookbook packages...

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Authors (1)

Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.

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