locuszoomr: an R package for visualizing publication-ready regional gene locus plots.

Area of Science:

• Genomics
• Bioinformatics
• Statistical Genetics

Background:

• Generating publication-quality genetic locus plots is crucial for visualizing genome-wide association study (GWAS) results.
• Existing tools often require web interfaces or lack flexibility in data integration and customization.

Purpose of the Study:

• To introduce locuszoomr, an R package for local, customizable, and publication-ready visualization of regional gene locus plots.
• To provide a flexible alternative to web-based tools for genetic data visualization.

Main Methods:

• Utilizes R base graphics or ggplot2 for plotting genetic data and gene annotation tracks.
• Integrates with the LDlink API for linkage disequilibrium (LD) data from the 1000 Genomes Project.
• Supports querying Ensembl databases for genomic information across multiple species and overlays recombination rate data.

Main Results:

• Locuszoomr enables modular plotting for layering multiple GWAS plots (e.g., PheWAS, eQTL comparisons) and aligning plots.
• Interactive plots can be generated using plotly for easy data point identification.
• The package demonstrates high performance, with rapid identification of GWAS peaks and plot generation.

Conclusions:

• Locuszoomr provides a powerful, flexible, and efficient R-based solution for genetic locus visualization.
• The package enhances reproducibility and customization in genetic data analysis and reporting.