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

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

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.

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

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

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

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

citation("gghic")

Minghao Jiang, [email protected]

gghic is licensed under the GNU General Public License v3.