Saturday, October 17, 2015

patPRO: Visualizing Longitudinal Microbiome Data

Recently some of my collaborators from the University of Pennsylvania and I released a new R package on CRAN (Comprehensive R Archive Network). It is called 'patPRO' (short for 'Patient Profiler'), and provides a number of functions to facilitate the visualization of longitudinal microbiome data. Although we developed it for examining changes in human microbiomes over time, it could just as easily be used for changes in microbial populations in water supplies, agricultural soils, or livestock, just to name a few possibilities.

This is an example of a plot that can be made, simultaneously showing changes in multiple dimensions of the microbiome:

Here is the official page for the package, with links to the reference manual and source code:

This link provides a version of the reference manual in a series of webpages:

- Brendan



Hannigan, G. D., M. A. Loesche, B. P. Hodkinson, S. Mehta, and E. A. Grice. 2015. patPRO: Visualizing Temporal Microbiome Data. R package version 1.0.0.
Download package (website)


Note: One implementation of R gave me an error indicating that 'stringi' was needed when I tried to install 'patPRO.' After installing 'stringi,' I ran across no further issues with patPRO.