#! /usr/bin/env Rscript
# DensiTree visualization of phylogenetic trees
args <- commandArgs(trailingOnly = TRUE)
if (length(args) != 6) {
  stop("Usage: Rscript 05.densitree.r <tree_file> <tip_order_file> <root> <output_pdf> <width> <height>")
}
tree_file <- args[1]
tip_order_file <- args[2]
root <- args[3]
output_pdf <- args[4]
width <- as.numeric(args[5])
height <- as.numeric(args[6])

library(ape)
library(phangorn)
trees <- read.tree(tree_file)
pdf(output_pdf, width = width, height = height)
for(i in 1:length(trees)) {
  trees[[i]] <- compute.brlen(root(trees[[i]], root))
}
tip_order <- rev(readLines(tip_order_file))
densiTree(trees, consensus=tip_order, alpha = 0.01,
  col = "#009900", type = "cladogram",
  label.offset = 0.02, scale.bar = FALSE
)
dev.off()