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Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Figure 4

Clustering accuracy in simulated two-class mixing.

Partitioning around medoids [49], [50] clustering accuracy (vertical axis) that results following different normalization and distance methods. Points denote the mean values of replicates, with a vertical bar representing one standard deviation above and below. Normalization method is indicated by both shade and shape, while panel columns and panel rows indicate the distance metric and median library size (), respectively. The horizontal axis is the effect size, which in this context is the ratio of target to non-target values in the multinomials that were used to simulate microbiome counts. Each multinomial is derived from two microbiomes that have negligible overlapping OTUs (Fecal and Ocean microbiomes in the Global Patterns dataset [48]). Higher values of effect size indicate an easier clustering task. For simulation details and precise definitions of abbreviations see Simulation A of the Methods section.

doi: https://doi.org/10.1371/journal.pcbi.1003531.g004