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

Anand Mayakonda^1,2, Frank Westermann^1,2

¹Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany.

Bioinformatics Advances

|March 13, 2024

Summary

Introducing trackplot, a fast R script for visualizing bigWig files. This tool generates IGV-style plots with minimal dependencies, significantly outperforming existing R packages for epigenomic data analysis.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

BigWig files are crucial for epigenomic data visualization.
Existing R packages for BigWig visualization are often slow and have many dependencies.

Purpose of the Study:

To introduce trackplot, a new R script for rapid generation of epigenomic data visualizations.
To address the limitations of current R packages for BigWig file visualization.

Main Methods:

trackplot utilizes bwtool for rapid data processing, achieving significant speed improvements.
The script generates Integrative Genomics Viewer (IGV)-style track plots, profile plots, and heatmaps.
It relies on minimal dependencies, including data.table and bwtool, and uses base R graphics.

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Main Results:

trackplot demonstrates performance gains of several magnitudes compared to existing R packages.
The script simplifies the visualization process by requiring only minimal dependencies.
It enhances reproducibility by querying the UCSC Genome Browser for gene models and supports General Transfer Format (GTF).

Conclusions:

trackplot offers a fast, simple, and lightweight solution for BigWig file visualization.
This tool significantly improves the efficiency of epigenomic data analysis and visualization.
trackplot is a valuable asset for researchers in epigenomics due to its speed and ease of use.