Compute tSNE position of samples from a phyloseq object
Arguments
- physeq
(required): a
phyloseq-class
object obtained using thephyloseq
package.- method
A method to calculate distance using
vegan::vegdist()
function- 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
)- ...
Other arguments passed on to
Rtsne::Rtsne()
Value
A list of element including the matrix Y containing the new representations for the objects. See ?Rtsne::Rtsne() for more information
Examples
if (requireNamespace("Rtsne")) {
res_tsne <- tsne_pq(data_fungi)
}
#> Taxa are now in rows.