gghic: A Versatile R Package for Exploring and Visualizing 3D Genome Organization

TL;DR

gghic is an R package that enhances visualization of 3D genome organization data, making complex chromatin interactions easier to interpret and integrate with genomic annotations for research and publication.

Contribution

It introduces new visualization layers for chromatin interactions and supports inter-chromosomal data, extending ggplot2 for genomic data analysis.

Findings

Successfully visualized a translocation event in T-ALL

Supports multiple chromosomes and inter-chromosomal interactions

Produces publication-quality figures

Abstract

Motivation: The three-dimensional (3D) organization of the genome plays a critical role in regulating gene expression and maintaining cellular homeostasis. Disruptions in this spatial organization can result in abnormal chromatin interactions, contributing to the development of various diseases including cancer. Advances in chromosome conformation capture technologies, such as Hi-C, have enabled researchers to study genome architecture at high resolution. However, the efficient visualization and interpretation of these complex datasets remain a major challenge, particularly when integrating genomic annotations and inter-chromosomal interactions. Results: We present gghic, an R package that extends the ggplot2 framework to enable intuitive and customizable visualization of genomic interaction data. gghic introduces novel layers for generating triangular heatmaps of chromatin interactions and annotating them with features such as chromatin loops, topologically associated domains (TADs), gene/transcript models, and data tracks (e.g., ChIP-seq signals). The package supports data from multiple chromosomes, facilitating the exploration of inter-chromosomal interactions. Built to integrate seamlessly with the R/Bioconductor ecosystem, gghic is compatible with widely used genomic data formats, including HiCExperiment and GInteractions objects. We demonstrate the utility of gghic by replicating a published figure showing a translocation event in T-cell acute lymphoblastic leukemia (T-ALL), highlighting its ability to integrate genomic annotations and generate publication-quality figures. Availability and implementation: The R package can be accessed at https://github.com/jasonwong-lab/gghic and is distributed under the GNU General Public License version 3.0.