(A) Partitioning by general body sites. Left, PERMANOVA F statistics for different indices when testing community distance partitioning according to general body site, i.e. into oral, skin, urogenital, airways and gastrointestinal habitats. Right, histograms of community distances intra-site (orange) and inter-site (blue) for all body sites against each other, oral against other habitats and gastrointestinal against other habitats. The inset illustrates how PERMANOVA F statistics and R2 values are calculated from community distances using the adonis function of the R package vegan (Anderson, 2001; Oksanen et al., 2015). (B) Sub-partitioning of oral habitats (blue), skin habitats (yellow) and urogenital habitats (violet). (C) Pairwise separation by different indices of all pairs of oral habitats, skin habitats against each other and against airways (anterior nares) and urogenital habitats against each other, as detected by the PERMANOVA R2 value (relative variance explained by factor habitat). Note the different color scales, indicating overall differential partitioning power per body site.
For more details and context, see http://biorxiv.org/content/early/2016/02/18/040097
For more details and context, see http://biorxiv.org/content/early/2016/02/18/040097