9.19 Plotting PBS trees

Another useful way to visualize PBS is by comparing trees for the top PBS outliers to the genome-wide average tree. Run the code blocks below to plot these trees:

# create average tree
tr_mean <- rtree(n = 3,
                 rooted = FALSE,
                 br = c(mean(pbs$T_rps_png),
                        mean(pbs$T_rps_chb),
                        mean(pbs$T_png_chb)))

# plot average tree
ggtree(tr_mean, layout = "daylight") +
  geom_treescale(width = 0.1) +
  geom_tiplab(label = c("RPS", "PNG", "CHB"))

## Average angle change [1] 0.333333333333333

## Average angle change [2] 2.22044604925031e-16

# create tree for top snp
tr_top <- rtree(n = 3,
                rooted = FALSE,
                br = c(pbs[1,]$T_rps_png,
                       pbs[1,]$T_rps_chb,
                       pbs[1,]$T_png_chb))

# plot top snp tree
ggtree(tr_top, layout = "daylight") +
  geom_treescale(width = 0.1) +
  geom_tiplab(label = c("RPS", "PNG", "CHB"))

## Average angle change [1] 0.333333333333333

## Average angle change [2] 2.22044604925031e-16