gghic

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

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

Author

Minghao Jiang, mjhk@connect.hku.hk

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, etc., under the heatmap.
5. Plot compartments, TADs, and loops on the heatmap.
6. Allow for generating rasterized heatmaps to handle large datasets.
7. Support duckplyr for faster data manipulation.
8. ...

Installation

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

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

Usage

You can find the vignettes for gghic by running the following command:

browseVignettes("gghic")

License

gghic is licensed under the GNU General Public License v3.