inst/docs/en/cookbook.md

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

Cookbook

Copy-paste recipes for common tasks. All examples use the bundled example_tree.

Color by a rank different from the collapse rank

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

Highlight a special ancestral node

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

Use exact custom colors

p <- plot_timetree(example_tree, rank = "phylum",
                   color_mapping = c("Firmicutes" = "#E41A1C",
                                     "Proteobacteria" = "#377EB8"),
                   unit = "Ma")

Put the legend on top with two columns

p <- plot_timetree(example_tree, rank = "phylum",
                   legend_position = "top", legend_ncol = 2, unit = "Ma")

Hide tip labels on a large tree

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

Draw as a cladogram (ignore branch lengths)

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

Detect label format before plotting

labels <- example_tree$tip.label
detect_taxonomy_format(labels)

Cross-validate a tree against a sequence file

validate_tree_sequence_match(example_tree, "seqs.fasta", mol_type = "DNA")

Check monophyly of a group

check_monophyly(example_tree, group = "Firmicutes", rank = "phylum")

Generate a palette for your own groups

groups <- c("Firmicutes", "Proteobacteria", "Bacteroidetes")
generate_colors(groups, palette = "viridis")

Enable detailed logging for a run

set_log_level("DEBUG")
set_log_file("rclade_run.log")
p <- plot_timetree(example_tree, rank = "phylum", unit = "Ma")

Time a pipeline stage

timer_start("collapse")
p <- plot_timetree(example_tree, rank = "phylum", unit = "Ma")
timer_stop("collapse")

Save a reproducible session record

save_session_info("session_info.txt")

See also Reference index.

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