Phylomorphospace plot with relative values

anilios.phylomopho.maker <- function(ypcs.df, means3d.df) {
  
    # make a subset of mean pca scores that we have tips for head shape 
    Ypcs.trim <- ypcs.df %>%
      semi_join(tree.tips, by = c('species' = 'species_in_tree'))
    # prune tree again for only tips that we have data for
    head_shape_df_tips <- as.vector(Ypcs.trim$species)
    # PRUNED tree for head shape data   
    Ypcs.trim.tree <- sub_mt_tree %>%
      keep.tip(., head_shape_df_tips)
    # PCA matrix for head shape 
    pca.headshape.matrix <- as.matrix(Ypcs.trim[c("mean_PC1", "mean_PC2")])
    rownames(pca.headshape.matrix) <- as.vector(Ypcs.trim$species)
  
  # plot layouts
  layout(matrix(c(1,2,2,
                  3,2,2,
                  4,5,6
                  ), 3, 3, byrow = TRUE),
         widths = c(1,1,2), heights = c(1,1,1))
  
  # plot extreme values
  means3d <- means3d.df
  Ypcs <- as.matrix(ypcs.df)
  # PC2max
  plotRefToTarget(mshape(means3d),
                  mshape(means3d[,,which(Ypcs[,2]==max(Ypcs[,2]))]))
  title(main = paste("max PC2", names(which(pca.headshape.matrix[,2]==max(pca.headshape.matrix[,2])))))

  # plot phylomorphospace of head shape data
  phylo_plot <- phylomorphospace(Ypcs.trim.tree, pca.headshape.matrix, label = "horizontal",
                                 fsize = 1,
                                 xlab = "Mean PC1", ylab = "Mean PC2",
                                 control = list(col.node=color.all))
  # PC2 min
  plotRefToTarget(mshape(means3d),
                  mshape(means3d[,,which(Ypcs[,2]==min(Ypcs[,2]))]))
  title(main = paste("min PC2", names(which(pca.headshape.matrix[,2]==min(pca.headshape.matrix[,2])))))
  
  plot.new()
  
  
  # PC1 max
  plotRefToTarget(mshape(means3d),
                  mshape(means3d[,,which(pca.headshape.matrix[,1]==max(pca.headshape.matrix[,1]))]))
  title(main = paste("max PC1", names(which(pca.headshape.matrix[,1]==max(pca.headshape.matrix[,1])))))
  
  # PC1 min
  plotRefToTarget(mshape(means3d),
                  mshape(means3d[,,which(Ypcs[,1]==min(Ypcs[,1]))]))
  title(main = paste("min PC1", names(which(pca.headshape.matrix[,1]==min(pca.headshape.matrix[,1])))))
  
  }


# Plot the phylomorphospace 
anilios.phylomopho.maker(ypcs.df = Ypcs.dorsal.df, means3d.df = means3d.dorsal)