phylogeo: an R package for geographic analysis and visualization of microbiome data

Bioinformatics. 2015 Sep 1;31(17):2909-11. doi: 10.1093/bioinformatics/btv269. Epub 2015 Apr 25.

Abstract

Motivation: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language.

Availability and implementation: phylogeo is documented and freely available http://zachcp.github.io/phylogeo

Contact: : zcharlop@rockefeller.edu.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computer Graphics*
  • Data Interpretation, Statistical
  • Humans
  • Metagenome*
  • Microbiota / genetics*
  • Phylogeny*
  • Programming Languages*
  • Sequence Analysis, DNA / methods*
  • Software*
  • Web Browser