phylogeo: an R package for geographic analysis and visualization of microbiome data. Academic Article uri icon

Overview

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 date

  • April 25, 2015

Research

keywords

  • Computer Graphics
  • Metagenome
  • Microbiota
  • Phylogeny
  • Programming Languages
  • Sequence Analysis, DNA
  • Software

Identity

PubMed Central ID

  • PMC4547612

Scopus Document Identifier

  • 84940758687

Digital Object Identifier (DOI)

  • 10.1093/bioinformatics/btv269

PubMed ID

  • 25913208

Additional Document Info

volume

  • 31

issue

  • 17