[Paper Review] gggenomes: effective and versatile visualizations for comparative genomics

Thomas Hackl, Markus J. Ankenbrand+3 more|arXiv (Cornell University)|Nov 5, 2024

Genetics, Bioinformatics, and Biomedical Research25 citations

TL;DR

gggenomes is an R package that extends ggplot2 to provide versatile visualizations for comparative genomics, addressing integration of diverse datasets and scalable, interactive-like plotting workflows. It is available on CRAN and GitHub with thorough documentation.

ABSTRACT

The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools often fail to efficiently integrate the diverse datasets produced in comparative genomics, lack intuitive interfaces to construct complex plots and are missing functionalities to inspect the underlying data iteratively and at scale. Here, we introduce gggenomes, a versatile R package designed to overcome these challenges by extending the widely used ggplot2 framework for comparative genomics. gggenomes is available from CRAN and GitHub, accompanied by detailed and user-friendly documentation (https://thackl.github.io/gggenomes).

Motivation & Objective

• Motivate the need for effective visualization of complex comparative genomics data.
• Propose a versatile R package that extends ggplot2 to streamline construction of multi-layer, integrative genomic plots.
• Provide accessible documentation and easy installation through CRAN and GitHub.

Proposed method

• Extend the ggplot2 framework with gggenomes to support comparative genomics visualizations.
• Address integration of diverse genomic datasets within a single, coherent plotting system.
• Emphasize intuitive interfaces for constructing complex plots and iterating over data at scale.

Experimental results

Research questions

• RQ1 How can visualization tools better integrate heterogeneous comparative genomics datasets within a unified plotting grammar?
• RQ2 What features are needed to construct and inspect complex genomic plots intuitively and at scale?
• RQ3 Does gggenomes provide a practical extension of ggplot2 for versatile comparative genomics visualizations?

Key findings

• gggenomes is a versatile R package designed to overcome common visualization challenges in comparative genomics.
• The package extends the ggplot2 framework to enable effective visualization of diverse genomic data.
• It is available from CRAN and GitHub with comprehensive documentation.