Trackplot: a fast and lightweight R script for epigenomic enrichment plots.

Abstract

BigWig files serve as essential inputs in epigenomic data visualization. However, current R packages for visualizing these files are limited, slow, and burdened by numerous dependencies. We introducetrackplot, a minimal R script designed for the rapid generation of integrative genomics viewer (IGV) style track plots, profile plots, and heatmaps from bigWig files. This script offers speed, owing to its reliance onbwtool, resulting in performance gains ofseveral magnitudescompared to equivalentpackages.The script is lightweight, requiring only thedata.tableandbwtoolpackages as primary dependencies. Notably, the plots are generated in base R graphics,eliminatingthe need for additional packages.trackplotqueries the University of California Santa Cruz (UCSC) genome browser for gene models thereby enhancing the reproducibility of analyses. The script extends its support to general transfer format (GTF) further enhancing its versatility. This tool addresses the gaps in existing bigWig visualization approaches by offering speed, simplicity, and minimal dependencies, thereby presenting a valuable asset to researchers in the fields of epigenomics. trackplot is implemented in R is made available under MIT license at https://github.com/PoisonAlien/trackplot.