Abstract
Summary: We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user’s session, allowing the user to archive, share and reproduce the sequence of steps that created their result—without writing any new code themselves.Availability and implementation: Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny-phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/.Contact: mcmurdie@alumni.stanford.edu.
Highlights
Analysis of microbial communities requires the interpretation of one or more high-dimensional abundance matrices and its relationship with other datasets, using a complex and emerging suite of methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing
R is well suited for the analytical aspects of microbiome research, with an interaction-oriented functional programming design (R Development Core Team, 2014) that includes support for reproducible research (Allaire et al, 2014; Xie, 2014)
We describe our release of ‘Shiny-phyloseq’, a Web browser graphical user interface (GUI) that leverages phyloseq and other R resources for the analysis of microbiome census data—while allowing the user to archive the complete code and data necessary to exactly reproduce their session results. It is difficult for any single GUI application to support the full range of analyses required in microbiome research, Shiny-phyloseq provides a compelling framework and introduction to microbiome analysis in R
Summary
Analysis of microbial communities requires the interpretation of one or more high-dimensional abundance matrices and its relationship with other datasets, using a complex and emerging suite of methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. We describe our release of ‘Shiny-phyloseq’, a Web browser GUI that leverages phyloseq and other R resources for the analysis of microbiome census data—while allowing the user to archive the complete code and data necessary to exactly reproduce their session results. It is difficult for any single GUI application to support the full range of analyses required in microbiome research, Shiny-phyloseq provides a compelling framework and introduction to microbiome analysis in R. There are no GUIs available for the analysis of microbiome census data that leverage the R programming language, ggplot (Wickham, 2009), and phyloseq while providing a ‘provenance record’ of a user’s session
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