Read taxonomy information from a table file — read_taxonomy_file • Rclade

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: ";".

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.

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).