gghic

A versatile R package for exploring and visualizing 3D genome organization

⚠️ gghic is in its early stages. Issues and PRs are welcome.

Introduction

gghic is a versatile R package for creating flexible, publication-ready visualizations of 3D genome organization data. With gghic, you can easily explore and present Hi-C/-like contact maps, topologically associating domains (TADs), chromatin loops, gene annotations, and other genomic features in a unified and customizable framework.

Whether you are analyzing large-scale Hi-C experiments, visualizing multi-chromosome interactions, or integrating additional genomic tracks (such as ChIP-seq or BigWig data), gghic provides a tidyverse-friendly and extensible toolkit for your research.

Features

1. Plot triangular heatmaps for genomic interaction data containing multiple chromosomes.
2. Plot chromosome ideograms with highlighted regions above the heatmap.
3. Plot gene/transcript model tracks under the heatmap.
4. Plot tracks of other genomic data, e.g., ChIP-seq peaks, BigWig files, concatemers, etc., under the heatmap.
5. Plot compartments, TADs, and loops on the heatmap.
6. Allow for generating rasterized heatmaps and tracks to handle large datasets.
7. Plot concatemers indicating multi-way contacts.
8. Support duckplyr for faster data manipulation.
9. ...

Installation

To install the gghic package from GitHub, use the following command:

devtools::install_github("jasonwong-lab/gghic", build_vignettes = TRUE)

Usage

• 📖 Documentation: Visit the gghic website for comprehensive documentation, tutorials, and examples.

• 📚 Vignettes: After installation, you can explore the package vignettes directly in R:

  browseVignettes("gghic")

Citation

citation("gghic")

Author

Minghao Jiang, mjhk@connect.hku.hk

License

gghic is licensed under the GNU General Public License v3.