plot_ordination display methods included in phyloseq.

<p>Each panel uses a “Bacteroidetes-only” subset of the preprocessed “Global Patterns” dataset that was also used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061217#pone-0061217-g004" target="_blank">Figure 4</a>. The coordinates are derived from an unconstrained correspondence analysis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061217#pone.0061217-Greenacre2" target="_blank">[62]</a>. Different panels illustrate different displays of the ordination results using the type argument to the plot_ordination function. (Top Left) Example of a samples-only display, with the “SampleType” mapped to the color aesthetic, and a filled-polygon layer to emphasize plot regions where sample types co-occur. (Top Left Insert) A “scree” plot of the eigenvalues associated with each axis, which indicates the proportion of total variability represented in each axis. (Top Right) Biplot representation in which samples and OTUs ordination results are overlaid. Clumps of OTUs appear to co-occur with different sample types, and some correlation with taxonomic phylum is also evident. (Middle) An OTUs-only plot that has been faceted (separated into panels) by class, with a two-dimensional density estimate overlain in blue. This view shows clearly a lack of association between the Sphingobacteria and Flavobacteria classes with fecal samples, which appear to be enriched in a subset of the Bacteroidia (relative to other OTUs in this Bacteroidetes-only dataset). Meanwhile, subsets of Bacteroidia appear to be enriched within multiple sample types. (Bottom) The “split” type for this graphic, in which both samples-only and OTUs-only plots are created, and shown side-by-side with one legend and shared vertical axis. Both the “biplot” and “split” options allow dual projections of both OTU- and sample-space.