tskit_arg_visualizer: interactive plotting of ancestral recombination graphs

TL;DR

The paper introduces tskit_arg_visualizer, a Python tool that uses interactive visualization to help researchers understand and explore ancestral recombination graphs, aiding both education and empirical data analysis.

Contribution

It presents a new Python package for programmatically visualizing ARGs with interactive features, enhancing understanding and analysis of complex genetic relationships.

Findings

Facilitates teaching of ARG concepts.

Enables exploration of empirically inferred ARGs.

Provides an accessible visualization tool for population genetics.

Abstract

Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent breakthroughs in simulation and inference methods have led to a surge of interest in ARGs. However, understanding how best to take advantage of the graphical structure of ARGs remains an open question for researchers. Here, we introduce tskit_arg_visualizer, a Python package for programmatically drawing ARGs using the interactive D3.js visualization library. We highlight the usefulness of this visualization tool for both teaching ARG concepts and exploring ARGs inferred from empirical datasets. Availability and implementation: The latest stable version of tskit_arg_visualizer is available through the Python Package Index (https://pypi.org/project/tskit-arg-visualizer, currently v0.1.0). Documentation and the development version of the package are found on GitHub (https://github.com/kitchensjn/tskit_arg_visualizer). Supplementary materials: Methods for creating the example ARGs seen in Figure 1 can be found in the supplementary materials.