Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison
Figure 5
The second principal component for the combined vaginal data, representing about 24 percent of the variance.
Low-weight regions of the tree are excluded from the figure. The edges across which maximal between-sample heterogeneity is found are those between two different Lactobacillus clades: L. iners and L. crispatus. Thus, the second important “axis” appears to correspond to the relative levels of these two species.