Fig. 5
Metabolome is Proximal to Phenotype on the Genotype-Phenotype Map (a) PCs 1 and 2 of > 3.2 × 105 LD-pruned variants (no missing calls, r2 < 0.5 within 50 kb windows) from the 16 genotypes in the metabolomics analysis. b PCs 1 and 2 of 2691 median normalized negative mode LC-MS features (corrected for batch and sample weight) from the same genotypes as in (a). In all plots, sensitive genotypes are colored in blue and resistant genotypes are colored in orange. The variance explained by each PC is shown in parentheses and the ellipses are the 50% confidence intervals. c Hierarchical clustering of the same genetic variants (c) or line mean values of the LC-MS features (d). Data were clustered using the minimal variance method (Ward’s D2) in the hclust R package