Plot a tsne low dimensional representation of a phyloseq object

Partially inspired by phylosmith::tsne_phyloseq() function developed by Schuyler D. Smith.

Usage

plot_tsne_pq(
  physeq,
  method = "bray",
  dims = 2,
  theta = 0,
  perplexity = 30,
  fact = NA,
  ellipse_level = 0.95,
  plot_dims = c(1, 2),
  na_remove = TRUE,
  force_factor = TRUE,
  ...
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

method

A method to calculate distance using vegan::vegdist() function (default: "bray")

dims

(Int) Output dimensionality (default: 2)

theta

(Numeric) Speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact TSNE (default: 0.0 see details in the man page of Rtsne::Rtsne).

perplexity

(Numeric) Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details in the man page of Rtsne::Rtsne)

fact

Name of the column in physeq@sam_data used to color points and compute ellipses.

ellipse_level

The level used in stat_ellipse. Set to NULL to discard ellipse (default = 0.95)

plot_dims

A vector of 2 values defining the rank of dimension to plot (default: c(1,2))

na_remove

(logical, default TRUE) Does the samples with NA values in fact are removed? (default: true)

force_factor

(logical, default TRUE) Force the fact column to be a factor.

...

Other arguments passed on to Rtsne::Rtsne()

Value

A ggplot object

Author

Adrien Taudière

Examples

data(data_fungi)
if (requireNamespace("Rtsne")) {
  plot_tsne_pq(data_fungi, fact = "Height", perplexity = 15)
}
#> Loading required namespace: Rtsne
#> Taxa are now in rows.

# \donttest{
if (requireNamespace("Rtsne")) {
  plot_tsne_pq(data_fungi, fact = "Time") + geom_label(aes(label = Sample_id, fill = Time))
  plot_tsne_pq(data_fungi, fact = "Time", na_remove = FALSE, force_factor = FALSE)
}
#> Taxa are now in rows.
#> Taxa are now in rows.

# }