6.3 Using ordr for PCA

The ordr package can be used to retain metadata (depths, labels, groups etc.) along with the PCA object. This is particularly useful for complex biplots using ggplot2. The following example uses the CD166_19_xrf_acomp_meta from the previous section; note that myElements is a vector of elements to include in the ordination, in this case generated in the section Noisy Data.

CD166_19_xrf_acomp_meta %>%
    ordr::ordinate(., cols = any_of(myElements),
                   model = ~ princomp(clr(.)),
                   augment = any_of(c("depth", "label"))
                   ) %>%
  ordr::ggbiplot(., sec.axes = "cols", scale.factor = 8) +
  ordr::geom_rows_point(aes(colour = depth, shape = label), alpha = 0.5) +
  ordr::geom_cols_vector() +
  ordr::geom_cols_text_radiate(aes(label = .name)) +
  scale_color_continuous(type = "viridis", trans = "reverse")