plot_ordination_pq: A wrapper of plot_ordination with vegan distance matrix

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

A wrapper of plot_ordination with vegan distance matrix

Description

A wrapper of plot_ordination with vegan distance matrix

Usage

plot_ordination_pq(
  physeq,
  method = "robust.aitchison",
  ordination_method = "NMDS",
  ...
)

Arguments

physeq	(required) a phyloseq-class object obtained using the phyloseq package.
method	(string, default "robust.aitchison") The distance method to use from vegan::vegdist(). See ?vegan::vegdist for more details.
ordination_method	(string, default "NMDS") The ordination method to use in phyloseq::ordinate(). See ?phyloseq::ordinate for more details.
...	Additional arguments passed on to phyloseq::plot_ordination()

Details

Basically a wrapper of phyloseq::plot_ordination() to use aitchison and robust.aitchison distances from vegan package.

Value

A ggplot2 object

Author(s)

Adrien Taudière

Examples

library(patchwork)
plot_ordination_pq(data_fungi_mini, method = "robust.aitchison", color = "Height") +
  plot_ordination_pq(data_fungi_mini, method = "bray", color = "Height")

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.