Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs

TL;DR

Snowflake is a new visualization tool that clearly shows all microbiome data, including rare taxa, helping researchers understand sample-specific and shared microbial patterns.

Contribution

Snowflake introduces a novel visualization method for microbiome abundance tables that retains all data and integrates hierarchical and metadata information.

Findings

Snowflake allows visualization of every observed OTU/ASV without data loss.

Experts found Snowflake user-friendly and useful for identifying sample-specific and shared taxa.

The method supports integrating alpha- and beta-diversity metrics and metadata into visualizations.

Abstract

Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data’s hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome’s composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.

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