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. 2023 Jan 1;39(1):btac786.
doi: 10.1093/bioinformatics/btac786.

GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data

Minsoo Kim  1   2   3 , Daniel D Vo  1 , Michi E Kumagai  1 , Connor T Jops  1 , Michael J Gandal  1   2   3   4   5
Affiliations

GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data

Minsoo Kim et al. Bioinformatics. .

Abstract

Summary: With the continued deluge of results from genome-wide association and functional genomic studies, it has become increasingly imperative to quickly combine and visualize different layers of genetic and genomic data within a given locus to facilitate exploratory and integrative data analyses. While several tools have been developed to visualize locus-level genetic results, the limited speed, scalability and flexibility of current approaches remain a significant bottleneck. Here, we present a Julia package for high-performance genetics and genomics-related data visualization that enables fast, simultaneous plotting of hundreds of association results along with multiple relevant genomic annotations. Leveraging the powerful plotting and layout utilities from Makie.jl facilitates the customization and extensibility of every component of a plot, enabling generation of publication-ready figures.

Availability and implementation: The GeneticsMakie.jl package is open source and distributed under the MIT license via GitHub (https://github.com/mmkim1210/GeneticsMakie.jl). The GitHub repository contains installation instructions as well as examples and documentation for built-in functions.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
A close look at the known pleiotropic GCKR locus using GeneticsMakie.jl. Index SNPs for phenotypes harboring GWAS hits are labeled and corresponding LD between other SNPs are displayed with the intensity of red color. Purple line denotes genome-wide significance (P = 5e−8), and yellow lines denote gene start and end sites for GCKR gene. Each GWAS result contains ∼3000 SNPs. The figure was generated on a personal lap-top (e.g. 2.3 GHz 8-Core Intel Core i9, 32 GB RAM) without any further modifications
See this image and copyright information in PMC

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