Fig. 4

PC2 vs. PC1 from kernel PCA on the microbiome kernel, colored by genotype of top variants from the significant genes in the HCHS/SOL study. For each variant, a 95% confidence ellipse (shown as a filled ellipse with black borders) was constructed for individuals from each genotype. The Bray-Curtis kernel was used for the top variant in the IL23R-C1orf141 region; the unweighted UniFrac kernel was used for the top variants in ZFR and MTMR12. The percent of variance captured by each kernel PC was provided in the axis labels. Panels B, D, and F show enlarged versions of the confidence ellipses from panels A, C, and E