3D-Manhattan: An interactive visualization tool for multiple GWAS results

Abstract

Genome-wide association studies (GWAS) are widely used to identify genetic loci underlying various agronomic traits. Conventional Manhattan plots provide an effective two-dimensional (2D) summary of an individual GWAS result. However, recent advances in high-throughput phenotyping have led to study designs that generate multiple GWAS outputs across time points, traits, or experimental conditions. In such settings, biological insight increasingly depends on comparative interpretation of multiple association maps, yet panel-based arrangements of 2D plots fragment related information and impede recognition of shared or dynamic genetic signals. Here, I present 3D-Manhattan, an interactive visualization framework that integrates multiple GWAS results within a unified three-dimensional (3D) coordinate system. By extending the conventional Manhattan plot with an additional axis representing time, trait, or condition, 3D-Manhattan enables simultaneous, axis-aligned comparison of association landscapes while preserving genomic coordinates and statistical values. The tool is implemented as a stand-alone, browser-based application using WebGL-based rendering and supports smooth interaction without server-side computation. The framework provides flexible visualization controls, region highlighting, and variant-level correspondence across datasets, facilitating exploratory analysis of stable and context-dependent genetic associations. Collectively, 3D-Manhattan provides an alternative approach for visualizing multi-dimensional GWAS results and offers a powerful platform for visualizing general a series of genome-wide datasets.