Publication-Ready Output
In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

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

Color-Blind Friendly Palettes

Rclade defaults to the viridis palette, which is: - Color-blind friendly - Grayscale friendly - Perceptually uniform

library(Rclade)
data(example_tree)

# Default viridis palette
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE)
print(p)

Custom Color Mapping

# Custom color mapping for specific groups
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE,
                   color_mapping = c("Proteobacteria" = "#E41A1C",
                                     "Firmicutes" = "#377EB8"))
print(p)

Legend Placement

# Inside the plot (default)
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE,
                   legend_position = c(0.05, 0.85))

# Standard positions
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE,
                   legend_position = "right")

Clade Labels

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

Taxonomy Quality Report

Before finalizing your figure, verify label parsing quality:

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

Batch Processing

Process multiple tree files at once:

batch_plot(input_dir = "trees/",
           output_dir = "figures/",
           pattern = "*.tre",
           rank = "phylum",
           taxonomy_format = "GTDB")

Reproducibility

save_session_info("session_info.txt")

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

The geological timescale data is based on the ICS International Chronostratigraphic Chart 2023/02 (https://stratigraphy.org/chart/).