treeHM.R

This script plots a circular phylogenetic tree with heatmap annotation.

Usage

Command line:

Rscript treeHM.R --tree data/test/test_tree.nwk --data data/test/test_heatmap_values.tsv --output data/test/test_output.pdf

• "-t", "--tree": Newick tree file
• "-d", "--data": TSV file, first column = leaves (matching tree tip labels), next columns = heatmap values
• "-o", "--output": Output PDF file (default: treeHM.pdf)

As a function in R:

source("treeHM.R")
tree <- ape::read.tree("tree.nwk")
hm_data <- read.table("data.tsv", header=TRUE, sep="\t", row.names=1, check.names=FALSE)
pdf("output.pdf", paper="A4")
print(create_hm_tree(tree, hm_data))
dev.off()

Example Output

Requirements

• R packages: ape, ggtree, ggplot2, ggnewscale, optparse

Features

• Warns about missing leaves and missing values.
• Supports both discrete and continuous heatmap columns.
• Output is always A4-sized PDF.