Graphic functions of the phyloseq package.

<p>The phyloseq class is an experiment-level data storage class defined by the phyloseq package for representing phylogenetic sequencing data. Most functions in the phyloseq package expect an instance of this class as their primary argument. See the phyloseq manual The Global Patterns <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061217#pone.0061217-Caporaso2" target="_blank">[47]</a> and Enterotypes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061217#pone.0061217-Arumugam1" target="_blank">[91]</a> datasets are included with the phyloseq package. The Global Patterns data was preprocessed such that each sample was transformed to the same total read depth, and OTUs were trimmed that were not observed at least 3 times in 20% of samples or had a coefficient of variation ≤ 3.0 across all samples. For the plot_tree and plot_bar subplots, only the Bacteroidetes phylum is shown. Each subplot title indicates the plot function that produced it. Complete details for reproducing this figure are provided in File S2. All of these functions return a ggplot object that can be further customized/modified by tools in the ggplot2 package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061217#pone.0061217-Wickham2" target="_blank">[57]</a>. See additional descriptions of each function in the body text, and at the phyloseq homepage <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061217#pone.0061217-The1" target="_blank">[39]</a>.