PangyPlot

PangyPlot simplifies exploration of pangenome graphs by retaining linear-style navigation, integrating gene annotations, abstracting complex variation into interpretable structures, and employing a dynamic, physics-based layout optimization engine.

Key Features:

• Linear-style navigation: Retains linear genome browser navigation patterns for pangenome graph exploration.
• Gene annotation integration: Incorporates gene annotations into pangenome graph visualization.
• Variation abstraction: Abstracts complex variation into interpretable structures.
• Dynamic physics-based layout optimization: Employs a physics-based engine for dynamic layout optimization of graph structures.
• Base-level and structural variation display: Displays both base-level and large structural variation in pangenome graphs.
• HPRC data preloading: Visualizes data from the Human Pangenome Reference Consortium (HPRC) pangenome graph.

Scientific Applications:

• Cystic fibrosis locus visualization: Visualizes cystic fibrosis-relevant loci in chromosome 7 graphs constructed from 101 individuals with cystic fibrosis.
• Structural variant fine-mapping: Fine-maps repeat-dense modifier loci using PacBio HiFi assemblies, as demonstrated for a chromosome 5 cystic fibrosis modifier locus.
• Repeat expansion identification: Identifies repeat expansions in gene regions, such as a repeat expansion in the 5 prime end of EXOC3 that may promote G-quadruplex formation and affect gene expression.
• Population-level variation interpretation: Makes population-level genetic variation interpretable through pangenome graph visualization.
• Graph viewer comparison: Enables comparison of pangenome graph visualization with existing graph viewers.

Methodology:

PangyPlot constructs chromosome-specific graphs from individual assemblies, uses a dynamic physics-based layout optimization engine for graph rendering, and integrates gene annotations with abstracted variation structures for visualization.