gghic

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

:warning: 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. [x] Plot triangular heatmaps for genomic interaction data containing multiple chromosomes.
2. [x] Plot chromosome ideograms with highlighted regions above the heatmap.
3. [x] Plot gene/transcript model tracks under the heatmap.
4. [x] Plot tracks of other genomic data, e.g., ChIP-seq peaks, BigWig files, concatemers, etc., under the heatmap.
5. [x] Plot compartments, TADs, and loops on the heatmap.
6. [x] Allow for generating rasterized heatmaps and tracks to handle large datasets.
7. [x] Plot concatemers indicating multi-way contacts.
8. [x] Use concatemers only to plot pairwise interactions.
9. [x] Plot a second heatmap below the main heatmap (lower triangle).
10. [x] Introduce a new S4 class ChromatinContacts for managing Hi-C/-like data.
11. [x] Check and suggest optimal resolutions based on sequencing depth.
12. [x] Build hypergraph representations from multi-way contact data.
13. [ ] Support duckplyr for faster data manipulation.
14. [ ] ...

Installation

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

devtools::install_github("jasonwong-lab/gghic")

Usage

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

Citation

citation("gghic")

Author

Minghao Jiang, [email protected]

License

gghic is licensed under the GNU General Public License v3.