20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
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+#! /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()