higlass-python: A programmable genome browser for linked interactive visualization and exploration of genomic data
Creators: name: Manz, Trevor
name: HiGlass Developers
name: Nezar Abdennur
name: Gehlenborg, Nils
Publisher: name: F1000 Research Limited
Year: 2023

description: HiGlass [1] is a web-based viewer designed for 1D and 2D genomic datasets. It provides smooth navigation through continuous zoom and pan interactions, and a flexible view configuration for traditional genome browser-like layouts. To further expand the capabilities of HiGlass and facilitate its integration with the scientific Python ecosystem, we have developed higlass-python, a software development kit (SDK) that enables the creation of custom HiGlass-powered applications and dashboards, as well as rapid exploration of genomic data in computational notebooks. A primary objective of higlass-python is to offer a versatile toolkit that enables synchronization between genomic representations within HiGlass and third-party visualizations presenting alternative representations of genomic loci. This distinctive feature, which is not typically available in other genome browsers, empowers computational researchers to quickly extend the genome browser using Python scripts. <br> <br> The majority of current genomic visualization tools focus on conventional representations of data mapped along the genome [1-3]; however, various complementary representations and summaries, such as scatter plots and embeddings, provide powerful exploratory lenses for comparative and integrative analysis of multi-omic datasets. Consequently, there is a growing need for a framework that can seamlessly integrate with traditional genome browser views and offer dynamically linked alternative views of the genome to facilitate a more complete exploration and analysis of genomic data. The higlass-python toolkit supplies building blocks to facilitate two-way data binding between HiGlass and other visualizations through single-locus mapping information. The third-party visualization can thereby access selections of genomic ranges within a HiGlass view and exercise control over the mapping of individual regional selections back to HiGlass.<br> <br> We employed our toolkit in computational notebook environments, such as Jupyter Notebooks, to examine the latent embedding spaces of 3D genomic contact frequency profiles within a functional and epigenomic context. The dimensionality-reduced representations of contact profiles are embedded into 2D visualizations where each point represents a genomic locus or interval. Our SDK coordinates multiple views of individual loci with HiGlass, demonstrating how individual selections of loci are synchronized across all views. A key feature of this use case is the ability to load, explore, export, and analyze the data all within the same computational environment. <br> <br> Finally, to streamline the development and utilization of higlass-python, we present anywidget, a tool designed to drastically simplify the creation of Jupyter widgets for both domain scientists with limited JavaScript (JS) experience and seasoned developers. Anywidget simplifies crafting interactive Jupyter visualizations that interface with HiGlass via our SDK, enabling diverse data representations for comprehensive genomic exploration. Although anywidget's capabilities extend beyond genomic visualizations, it proves highly useful in this context.<br> <br> <br> [1] Kerpedjiev, et al. (2018). HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biology.<br> [2] Buels, et al. (2016). JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biology.<br> [3] Thorvaldsdóttir, et al. (2013). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics.