MetaCarto: biologically faithful automatic layout for genome-scale metabolic maps
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Motivation
Genome-scale metabolic reconstructions containing thousands of reactions are now curated and published for many organisms, but their visualization still relies heavily on manually constructed pathway maps. As these models grow in size and number, an automatic method is needed to organize their reactions into readable maps for visualization and downstream analysis.
Results
We developed M eta C arto , an automatic layout framework for genome-scale metabolic maps. M eta C arto identifies a biologically meaningful primary connection for each reaction and then organizes these connections into readable pathway-scale layouts, separating the biological representation of a reaction from its geometric placement. The resulting maps show strong agreement with curated KEGG pathway representations while maintaining geometric quality comparable to established graph-layout approaches. We applied M eta C arto to all 108 BiGG models and generated 2621 pathway maps without manual rearrangement. As a large-scale example, the human Recon3D reconstruction, containing 10 600 reactions, was automatically decomposed into 93 maps and laid out in 107 s. The generated maps are exported as Escher-compatible JSON and SVG files and can be directly browsed, edited, and used for metabolic data visualization.
Availability and implementation
Source code is available under CC BY 4.0 at github.com/forxhunter/MetaCarto. The complete collection of generated maps is available at GitHub map collection and can be browsed interactively at forxhunter.github.io/escher.
Contact
tianyu16@illinois.edu
Supplementary information
Supplementary data are available at github.com/forxhunter/MetaCarto.
