Add phylogenetic tree to MDS plot of leaves in R

add_tree_to_mapping.R

     poEdge <- Postorder(tree())$edge
     parent <- poEdge[, 1]
     child <- poEdge[, 2]
     xy <- matrix(0, parent[1], 2)
     xy[seq_len(NTip(tree())), ] <- mapping()
     for (node in unique(parent)) {
       xy[node, ] <- colMeans(xy[child[parent == node], , drop = FALSE])
     }
     segments(xy[parent, 1], xy[parent, 2],
              xy[child, 1], xy[child, 2],
              col = "#00000033")
     points(xy[parent, 1], xy[parent, 2], pch = ".", col = "#00000099")