Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data-Reference-Cited by-同舟云学术

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data

Published:2021-10-26 Issue:5 Volume:6 Page:
ISSN:2379-5077
Container-title:mSystems
language:en
Short-container-title:mSystems

Author:

Armstrong George¹²³,Martino Cameron¹²³^ORCID,Rahman Gibraan¹³,Gonzalez Antonio¹,Vázquez-Baeza Yoshiki²,Mishne Gal⁴⁵,Knight Rob¹⁵⁶^ORCID

Affiliation:

1. Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA

2. Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA

3. Bioinformatics and Systems Biology Program, University of California, San Diego, California, USA

4. Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA

5. Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA

6. Department of Bioengineering, University of California, San Diego, La Jolla, California, USA

Abstract

UMAP provides an additional method to visualize microbiome data. The method is extensible to any beta diversity metric used with PCoA, and our results demonstrate that UMAP can indeed improve visualization quality and correspondence with biological and technical variables of interest.

Funder

International Business Machines Corporation

Publisher

American Society for Microbiology

Subject

Computer Science Applications,Genetics,Molecular Biology,Modelling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology

Link

https://journals.asm.org/doi/pdf/10.1128/mSystems.00691-21

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