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


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


BACKGROUND
: zcharlop@rockefeller.edu.
Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA.
Zachary
Z
Charlop-Powers
Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA.
Sean F
SF
Brady
D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D006801:Humans; D054892:Metagenome; D064307:Microbiota / Q000235:genetics*; D010802:Phylogeny; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D064878:Web Browser