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

SUMMARY

Locuszoomr is an R package for visualizing and creating publication-ready regional gene locus plots similar to those produced by the original web interface 'LocusZoom', but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics or 'ggplot2', allowing flexibility and easy customization. Modular plotting functions enable layering of multiple GWAS plots such as for PheWAS, comparing GWAS with eQTL signals, and aligning multiple locus plots on the same page. Interactive plots can be visualized using 'plotly' enabling quick identification of data points for labelling. The 'LDlink' API (https://ldlink.nih.gov/) can be programmatically queried to obtain linkage disequilibrium (LD) data from the 1000 Genomes Project which is overlaid on plots. The package allows users to query Ensembl databases from Bioconductor or AnnotationHub for genomic information, so it can be used to show gene track information for any species available in Ensembl. Helper functions enable recombination rate data from UCSC to be overlaid on plots. The package has a detailed vignette and includes embedded example GWAS data to allow users to try out different features. Locuszoomr is also fast: identifying 50 peaks in a GWAS of around 8 million SNPs takes around 0.6 s. Exporting 50 locus plots with 1 Mb window with recombination rate takes around 30 son Intel ninth gen CPU or 14 son Apple ARM M3.

AVAILABILITY AND IMPLEMENTATION

The R package locuszoomr is open-source and available from CRAN: https://cran.r-project.org/package=locuszoomr and GitHub: https://github.com/myles-lewis/locuszoomr.