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")
#> Taxa are now in columns.
#> Run 0 stress 0.115973 
#> Run 1 stress 0.1300024 
#> Run 2 stress 0.1183097 
#> Run 3 stress 0.1214998 
#> Run 4 stress 0.133196 
#> Run 5 stress 0.1530583 
#> Run 6 stress 0.1430454 
#> Run 7 stress 0.1300024 
#> Run 8 stress 0.1187081 
#> Run 9 stress 0.1381296 
#> Run 10 stress 0.1267024 
#> Run 11 stress 0.1188736 
#> Run 12 stress 0.1443663 
#> Run 13 stress 0.1182422 
#> Run 14 stress 0.118866 
#> Run 15 stress 0.1188301 
#> Run 16 stress 0.130007 
#> Run 17 stress 0.1247712 
#> Run 18 stress 0.1386751 
#> Run 19 stress 0.1159623 
#> ... New best solution
#> ... Procrustes: rmse 0.001485213  max resid 0.01705792 
#> Run 20 stress 0.1381296 
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#>     13: stress ratio > sratmax
#>      7: 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>.
#> Taxa are now in columns.
#> Run 0 stress 0.1894383 
#> Run 1 stress 0.1888345 
#> ... New best solution
#> ... Procrustes: rmse 0.0524328  max resid 0.2341065 
#> Run 2 stress 0.1901206 
#> Run 3 stress 0.1855488 
#> ... New best solution
#> ... Procrustes: rmse 0.05964591  max resid 0.2629411 
#> Run 4 stress 0.1884944 
#> Run 5 stress 0.1886409 
#> Run 6 stress 0.1865063 
#> Run 7 stress 0.1873102 
#> Run 8 stress 0.190706 
#> Run 9 stress 0.1873528 
#> Run 10 stress 0.1882318 
#> Run 11 stress 0.189307 
#> Run 12 stress 0.1896571 
#> Run 13 stress 0.1864311 
#> Run 14 stress 0.1893721 
#> Run 15 stress 0.1854113 
#> ... New best solution
#> ... Procrustes: rmse 0.01940789  max resid 0.1180019 
#> Run 16 stress 0.1904496 
#> Run 17 stress 0.1869919 
#> Run 18 stress 0.1887375 
#> Run 19 stress 0.1902213 
#> Run 20 stress 0.1902424 
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#>     14: no. of iterations >= maxit
#>      6: stress ratio > sratmax