Quick Start: From Tree File to Publication Figure
In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 10,
  fig.height = 7
)

Installation

# Install from local source package
install.packages("path/to/Rclade_1.0.0.tar.gz", repos = NULL, type = "source")

Basic Usage

The simplest way to create a timetree visualization using the built-in example data:

library(Rclade)

# Load built-in example tree (50 tips, GTDB-style labels)
data(example_tree)

# Plot with phylum-level collapsing (no timescale for speed)
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE)
print(p)

Adding Titles

Use main_title and sub_title to add centered titles:

p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE,
                   main_title = "GTDB Bacterial Tree",
                   sub_title = "50 taxa | Phylum-level collapsing")
print(p)

Summarizing Results

Use summarize_timetree() to inspect the collapse metadata:

p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE)
summarize_timetree(p)

Saving Output

# Save to PDF
save_timetree(p, "output.pdf", width = 14, height = 10)

# One-line pipeline
# Note: the geological timescale requires an explicit branch-length unit
# (Rclade does not infer units); pass unit = "Ma" or unit = "Ga".
plot_timetree(example_tree, rank = "phylum", unit = "Ga", output = "output.pdf")

Taxonomy Quality Check

Before visualization, check how well your labels can be parsed:

summarize_taxonomy_quality(example_tree$tip.label, format = "GTDB")

References & Acknowledgments

Rclade builds on the ggtree and deeptime R packages. If you use Rclade in published research, please cite Rclade along with these key dependencies:

Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y (2017). "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data." Methods in Ecology and Evolution, 8(1), 28-36. doi:10.1111/2041-210X.12628
Gearty W (2025). "deeptime: an R package that facilitates highly customizable and reproducible visualizations of data over geological time intervals." Big Earth Data. doi:10.1080/20964471.2025.2537516
Paradis E, Schliep K (2019). "ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R." Bioinformatics, 35(3), 526-528. doi:10.1093/bioinformatics/bty633