A wrapper of plot_ordination with vegan distance matrix

Usage

plot_ordination_pq(
  physeq,
  method = "robust.aitchison",
  ordination_method = "NMDS",
  add_envfit = FALSE,
  envfit_fact = NULL,
  envfit_pval = 1,
  envfit_arrow_mult = 1,
  envfit_text_size = 3,
  envfit_col = "black",
  ...
)

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.
add_envfit: (logical, default FALSE) If TRUE, overlay environmental vectors (and factor centroids) fitted to the ordination using vegan::envfit(). Continuous variables are shown as arrows and factor variables as labelled centroids.
envfit_fact: (default NULL) A character vector of variable names from physeq@sam_data to fit onto the ordination. When NULL (default) and add_envfit = TRUE, every variable of physeq@sam_data is used; passing an explicit subset is recommended, as fitting identifier or high-cardinality character columns produces a cluttered overlay.
envfit_pval: (float, default 1) Only environmental variables with an vegan::envfit() p-value lower than or equal to this threshold are drawn. The default (1) draws all of them.
envfit_arrow_mult: (float, default 1) A multiplier applied to the environmental arrow lengths, to scale them for readability.
envfit_text_size: (float, default 3) Text size for the environmental variable labels.
envfit_col: (default "black") Color of the environmental arrows, centroids and labels.
...: 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 0.1325369 
#> Run 2 stress 0.1266062 
#> Run 3 stress 0.1159623 
#> ... New best solution
#> ... Procrustes: rmse 0.001484698  max resid 0.01705622 
#> Run 4 stress 0.4017493 
#> Run 5 stress 0.1159623 
#> ... New best solution
#> ... Procrustes: rmse 2.727712e-05  max resid 0.0002491861 
#> ... Similar to previous best
#> Run 6 stress 0.1330352 
#> Run 7 stress 0.1182422 
#> Run 8 stress 0.1443908 
#> Run 9 stress 0.1399469 
#> Run 10 stress 0.1178904 
#> Run 11 stress 0.1242026 
#> Run 12 stress 0.4057599 
#> Run 13 stress 0.1247709 
#> Run 14 stress 0.1244501 
#> Run 15 stress 0.1159624 
#> ... Procrustes: rmse 8.367899e-05  max resid 0.0006713144 
#> ... Similar to previous best
#> Run 16 stress 0.1300559 
#> Run 17 stress 0.1266062 
#> Run 18 stress 0.118866 
#> Run 19 stress 0.1266066 
#> Run 20 stress 0.1267024 
#> *** Best solution repeated 2 times
#> 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 0.1894178 
#> Run 1 stress 0.1902982 
#> Run 2 stress 0.1885288 
#> ... New best solution
#> ... Procrustes: rmse 0.07195784  max resid 0.2513823 
#> Run 3 stress 0.1906335 
#> Run 4 stress 0.1886527 
#> ... Procrustes: rmse 0.04927937  max resid 0.1896001 
#> Run 5 stress 0.1884407 
#> ... New best solution
#> ... Procrustes: rmse 0.05666386  max resid 0.2401529 
#> Run 6 stress 0.1895027 
#> Run 7 stress 0.188027 
#> ... New best solution
#> ... Procrustes: rmse 0.04457651  max resid 0.209187 
#> Run 8 stress 0.1902578 
#> Run 9 stress 0.1894697 
#> Run 10 stress 0.1911124 
#> Run 11 stress 0.1901589 
#> Run 12 stress 0.1889636 
#> Run 13 stress 0.1894248 
#> Run 14 stress 0.1909407 
#> Run 15 stress 0.1891702 
#> Run 16 stress 0.1870773 
#> ... New best solution
#> ... Procrustes: rmse 0.0770278  max resid 0.2988579 
#> Run 17 stress 0.1878373 
#> Run 18 stress 0.189832 
#> Run 19 stress 0.1898224 
#> Run 20 stress 0.1885919 
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#>     14: no. of iterations >= maxit
#>      6: stress ratio > sratmax

# \donttest{
plot_ordination_pq(
  subset_samples(data_fungi_mini, !is.na(Height)),
  method = "bray",
  color = "Height",
  add_envfit = TRUE,
  envfit_fact = "Time"
)
#> Taxa are now in columns.
#> Run 0 stress 0.1519287 
#> Run 1 stress 0.1531429 
#> Run 2 stress 0.1537355 
#> Run 3 stress 0.1532178 
#> Run 4 stress 0.1493505 
#> ... New best solution
#> ... Procrustes: rmse 0.09344892  max resid 0.4339096 
#> Run 5 stress 0.1518891 
#> Run 6 stress 0.1496581 
#> ... Procrustes: rmse 0.05159805  max resid 0.2239141 
#> Run 7 stress 0.1494295 
#> ... Procrustes: rmse 0.04119706  max resid 0.2142381 
#> Run 8 stress 0.1514083 
#> Run 9 stress 0.1520738 
#> Run 10 stress 0.1524282 
#> Run 11 stress 0.1502924 
#> Run 12 stress 0.1540894 
#> Run 13 stress 0.1495954 
#> ... Procrustes: rmse 0.04991083  max resid 0.2124419 
#> Run 14 stress 0.1534718 
#> Run 15 stress 0.1518599 
#> Run 16 stress 0.1520461 
#> Run 17 stress 0.1509607 
#> Run 18 stress 0.1529119 
#> Run 19 stress 0.1502318 
#> Run 20 stress 0.1528109 
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#>     20: no. of iterations >= maxit

# }