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()

Value

A ggplot2 object

Details

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

Author

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")
#> Run 0 stress 0.1133285 
#> Run 1 stress 0.1810546 
#> Run 2 stress 0.124062 
#> Run 3 stress 0.197421 
#> Run 4 stress 0.1846916 
#> Run 5 stress 0.1436983 
#> Run 6 stress 0.1467497 
#> Run 7 stress 0.1342782 
#> Run 8 stress 0.1292872 
#> Run 9 stress 0.1379121 
#> Run 10 stress 0.1724095 
#> Run 11 stress 0.1834184 
#> Run 12 stress 0.1815515 
#> Run 13 stress 0.1937242 
#> Run 14 stress 0.2003058 
#> Run 15 stress 0.1779367 
#> Run 16 stress 0.1691389 
#> Run 17 stress 0.2030561 
#> Run 18 stress 0.1506576 
#> Run 19 stress 0.1557108 
#> Run 20 stress 0.1798924 
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#>     14: stress ratio > sratmax
#>      6: scale factor of the gradient < sfgrmin
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the phyloseq package.
#>   Please report the issue at <https://github.com/joey711/phyloseq/issues>.
#> Run 0 stress 0.2437839 
#> Run 1 stress 0.2503454 
#> Run 2 stress 0.2449217 
#> Run 3 stress 0.2488405 
#> Run 4 stress 0.2506359 
#> Run 5 stress 0.2449691 
#> Run 6 stress 0.2459483 
#> Run 7 stress 0.2462621 
#> Run 8 stress 0.2468937 
#> Run 9 stress 0.2459695 
#> Run 10 stress 0.2500868 
#> Run 11 stress 0.2483659 
#> Run 12 stress 0.2463637 
#> Run 13 stress 0.244415 
#> Run 14 stress 0.2485833 
#> Run 15 stress 0.248111 
#> Run 16 stress 0.2485444 
#> Run 17 stress 0.2484063 
#> Run 18 stress 0.2518243 
#> Run 19 stress 0.2474289 
#> Run 20 stress 0.2454506 
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#>      1: no. of iterations >= maxit
#>     19: stress ratio > sratmax