inst/docs/en/getting-started.md

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

Getting Started

This guide walks you through your first Rclade plot in five minutes.

1. Load the package and the example data

library(Rclade)
data(example_tree)   # a phylo object with GTDB-style tip labels

example_tree is a small bundled tree so you can try everything without your own data.

2. Draw your first time tree

Collapse the tree at the phylum rank and add a geological timescale:

p <- plot_timetree(example_tree, rank = "phylum", unit = "Ma")
print(p)

That single call:

1. detects the taxonomy format from the tip labels,
2. parses each tip's phylum,
3. finds the MRCA of each phylum and collapses it into a triangle,
4. adds the geological timescale on the x-axis,
5. assigns a color-blind-safe palette and lays out the legend.

3. Save the figure

save_timetree(p, file = "phylum_tree.pdf", width = 12, height = 8)

Formats are chosen by file extension: .pdf, .png, .tiff, .svg, .eps.

4. Inspect what happened

summarize_timetree(p)

This prints the number of tips, collapsed clades, taxonomy coverage, and more.

5. Try common variations

# Circular / fan layout
p2 <- plot_timetree(example_tree, rank = "class", layout = "circular")

# Turn off the timescale
p3 <- plot_timetree(example_tree, rank = "phylum", add_timescale = FALSE)

# Use a custom palette
p4 <- plot_timetree(example_tree, rank = "phylum", color_palette = "Set1")

6. Go further

• Plot many trees at once: batch_plot
• Parse and validate your own labels: Taxonomy Parsing
• Run from the command line: run_rclade_cli
• Use the graphical app: run_rclade_shiny

Next: read Core concepts to understand taxonomy formats, MRCA collapsing, and timescales.

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.