BiomeHorizon: Visualizing Microbiome Time Series Data in R

Isaac Fink, Richard J Abdill, Ran Blekhman, Laura Grieneisen

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Despite playing a key role in the health of their hosts, host-associated microbial communities demonstrate considerable variation over time. These communities comprise thousands of temporally dynamic taxa, which makes visualizing microbial time series data challenging. As such, a method to visualize both the proportional and absolute change in the relative abundance of multiple taxa across multiple subjects over time is needed. To address this gap, we developed BiomeHorizon, the first automated, open-source R package that visualizes longitudinal compositional microbiome data using horizon plots. BiomeHorizon is available at https://github.com/blekhmanlab/biomehorizon/ and a guide with step-by-step instructions for using the package is provided at https://blekhmanlab.github.io/biomehorizon/.

Original languageEnglish (US)
JournalmSystems
Volume7
Issue number3
DOIs
StatePublished - Jun 2022

Bibliographical note

Funding Information:
We thank members of the Blekhman Lab, especially Sambhawa Priya, for comments on the tutorial. We also thank Abigail Johnson and members of the Amboseli Baboon Research Project, especially Susan Alberts, Beth Archie, and Jenny Tung, for generating the publicly available data sets used in the package. This work was supported by the National Institute of Health (NIH R35-GM128716 to R.B.) and the University of Minnesota Grand Challenges in Biology Postdoctoral Fellowship to L.G.

Publisher Copyright:
© 2022 Fink et al.

Keywords

  • R package
  • microbiome
  • time series
  • Microbiota
  • Animals, Wild
  • Animals
  • Time Factors
  • Humans
  • Bacteria
  • Research Design

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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