read_taxonomy_file: Read taxonomy information from a table file

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

Read taxonomy information from a table file

Description

Reads taxonomy information from a two-column table file where:

• Column 1: Tip labels (must match tree tip labels)

• Column 2: Taxonomy strings in GTDB format (e.g., d__Archaea;p__Thermoproteota;c__Korarchaeia)

Usage

read_taxonomy_file(file, sep = "auto", header = FALSE, table_sep = ";")

Arguments

file	Character. Path to the taxonomy table file.
sep	Character. Column separator. "auto" auto-detects tab or comma. Default: "auto".
header	Logical. Whether the file has a header row. Default: FALSE.
table_sep	Character. Separator between taxonomy ranks in the second column (the taxonomy string). Default: ";".

Details

Supports tab-delimited or comma-delimited files. Missing ranks are indicated by empty values after the rank prefix (e.g., s__ for missing species).

Value

A data.frame with columns:

label

Character. Tip labels from column 1.

domain

Character. Domain (d__).

phylum

Character. Phylum (p__).

class

Character. Class (c__).

order

Character. Order (o__).

family

Character. Family (f__).

genus

Character. Genus (g__).

species

Character. Species (s__).

Missing ranks are NA.

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