phylogeo：一个用于微生物组数据地理分析和可视化的R软件包。
phylogeo: an R package for geographic analysis and visualization of microbiome data.
作者信息
Charlop-Powers Zachary, Brady Sean F
机构信息
Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA.
出版信息
Bioinformatics. 2015 Sep 1;31(17):2909-11. doi: 10.1093/bioinformatics/btv269. Epub 2015 Apr 25.
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
动机
我们创建了一个名为phylogeo的R包，它为基于测序的微生物生态学研究提供了一组地理实用工具。尽管样本的地理位置是环境微生物学的一个重要方面，但处理微生物组数据时使用的主要软件包中，没有一个包含允许用户绘制和探索其数据空间维度的实用工具。phylogeo通过提供一组绘图和映射函数来解决这个问题，这些函数可用于可视化样本的地理分布，使用生态距离查看微生物群落的相关性，以及绘制特定序列的地理分布。通过扩展流行的phyloseq包并使用相同的数据结构和命令格式，phylogeo允许用户从R编程语言轻松地绘制和探索其数据的地理维度。
可用性和实现
phylogeo有文档记录且可从http://zachcp.github.io/phylogeo免费获取。
Zotero 插件