plot_gtdb_tr: Plot GTDB-Tk Phylogenetic Tree with Taxonomic Coloring

In pctax: Professional Comprehensive Omics Data Analysis

Plot GTDB-Tk Phylogenetic Tree with Taxonomic Coloring

Description

This function creates a circular phylogenetic tree visualization from GTDB-Tk results, with tips colored by specified taxonomic level. It can optionally represent only one genome per species.

Usage

plot_gtdb_tr(
  gtdb_res,
  tree,
  tax_level = "Phylum",
  represented = TRUE,
  layout = "fan",
  branch_size = 0.2,
  color_na = "black"
)

Arguments

gtdb_res	A data frame containing GTDB-Tk classification results, typically the output from pre_gtdb_tk function.
tree	A phylogenetic tree object (phylo class) containing all genomes.
tax_level	Character specifying the taxonomic level for coloring tips. Default is "Phylum". Other options include "Class", "Order", "Family", "Genus", "Species".
represented	Logical indicating whether to include only one representative genome per species. Default is TRUE.
layout	Character specifying the tree layout. Options include "fan", "circular", "rectangular", etc. Default is "fan".
branch_size	Numeric value for branch line width. Default is 0.2.
color_na	Character specifying color for tips with missing taxonomic information. Default is "black".

Value

A ggplot object containing the phylogenetic tree visualization.

pctax documentation built on Feb. 9, 2026, 9:06 a.m.