rotl_pq: rotl wrapper for phyloseq data

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

rotl wrapper for phyloseq data

Description

Make a phylogenetic tree using the ASV names of a physeq object and the Open Tree of Life tree.

Usage

rotl_pq(physeq, species_colnames = "Genus_species", context_name = "All life")

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
species_colnames	(default: "Genus_species"): the name of the column where the species binominal name is stored in ⁠@tax_table⁠ slot. Can also be a vector of two columns names e.g. c("Genus", "Species")
context_name	: can bue used to select only a part of the Open Tree of Life. See ?rotl::tnrs_contexts() for available values

Details

This function is mainly a wrapper of the work of others. Please make a reference to rotl package if you use this function.

Value

A plot

Author(s)

Adrien Taudière

Examples

if (requireNamespace("rotl")) {
  tr <- rotl_pq(data_fungi_mini, species_colnames = "Genus_species")
  plot(tr)

  tr_Asco <- rotl_pq(data_fungi, species_colnames = "Genus_species", context_name = "Ascomycetes")
  plot(tr_Asco)
}

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.