Modify default aboot plotting function in R

mod_poppr_plot_phylo.R

# poppr.plot.phylo definition:
# https://github.com/grunwaldlab/poppr/blob/9170398f6552f27ab69b294172c97c8ee7a97ce0/R/internal.r#L1529-L1545
# You can also get it by simply typing poppr:::poppr.plot.phylo in your R console
library("ape")
library("phangorn")
poppr.plot.phylo <- function(tree, type = "nj", root = FALSE){
  barlen <- min(median(tree$edge.length), 0.1)
  if (barlen < 0.1) barlen <- 0.01
  if (!root && type != "upgma"){
    tree <- ladderize(tree)
  }
  nodelabs <- round(tree$node.label, 2)
  plot.phylo(tree, cex = 1, font = 2, adj = 0, xpd = TRUE, 
             label.offset = 0.0125)
  nodelabels(nodelabs, adj = c(1.3, -0.5), frame = "n", cex = 0.8, 
             font = 3, xpd = TRUE)
  if (type != "upgma"){
    add.scale.bar(lwd = 5, length = barlen)
  } else {
    axisPhylo(3)
  }
}

assignInNamespace("poppr.plot.phylo", poppr.plot.phylo, ns = "poppr")