Design Space and Declarative Grammar for 3D Genomic Data Visualization

Various computational approaches predict chromatin structure, yielding concrete models that position genomic loci in physical space and help reveal genome organization and function. While prior visualization research has explored data and task abstractions for genomics, the design space for depicting these three-dimensional (3D) genome models-and associated genome-mapped data-remains unclear. In this paper, we investigate the visualization of genomic data with a spatial component. First, we systematically survey how 3D genome models are used and depicted in computational biology. We analyze over 300 papers with figures that visualize 3D genomic data and categorize the methods for visual representation. From this survey, we derive a design space for visualizing 3D genome data, identifying common patterns and key properties such as representation, visual channels, and composition. We position these findings within an existing genomics visualization taxonomy, refining and extending existing classifications. Second, we augment Gosling, a declarative visualization grammar for genomics, to support 3D genomic data. Our integration enables expressive authoring of visualizations that connect traditional genome-mapped information with 3D genome models, emphasizing their spatial characteristics. To demonstrate its utility, we employ our extended grammar to recreate interactive examples, showcasing its ability to represent complex visual designs. Comprehensive examples and an interactive editor are available at 3d.gosling-lang.org.