gghic：用于探索和可视化三维基因组组织的多功能 R 包
gghic: A Versatile R Package for Exploring and Visualizing 3D Genome Organization
AI总结：
本文提出 R 包 gghic，基于 ggplot2 提供染色质相互作用三角形热图、TAD/基因/ChIP-seq 注释及染色体间数据可视化，并以 T-ALL 易位图验证其发表级绘图能力。
摘要：
动机：基因组的三维（3D）组织在调控基因表达和维持细胞稳态方面发挥着关键作用。这种空间组织的破坏可能导致异常的染色质相互作用，从而促进包括癌症在内的多种疾病的发生。Hi-C 等染色体构象捕获技术的进展使研究人员能够以高分辨率研究基因组结构。然而，高效可视化和解释这些复杂数据集仍是一项重大挑战，尤其是在整合基因组注释和染色体间相互作用时。结果：我们提出 gghic，这是一个扩展 ggplot2 框架的 R 包，可实现基因组相互作用数据的直观且可定制的可视化。gghic 引入了新的图层，用于生成染色质相互作用的三角形热图，并使用染色质环、拓扑关联结构域（TADs）、基因/转录本模型和数据轨道（例如 ChIP-seq 信号）等特征对其进行注释。该包支持来自多条染色体的数据，促进了对染色体间相互作用的探索。gghic 专为与 R/Bioconductor 生态系统无缝集成而构建，兼容广泛使用的基因组数据格式，包括 HiCExperiment 和 GInteractions 对象。我们通过复现一幅已发表的、展示 T 细胞急性淋巴细胞白血病（T-ALL）中易位事件的图来证明 gghic 的实用性，突显其整合基因组注释并生成可发表质量图形的能力。可用性与实现：该 R 包可在 https://github.com/jasonwong-lab/gghic 获取，并依据 GNU General Public License version 3.0 发布。
英文摘要：
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.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
