View source: R/plot_functions.R
plot_tsne_pq | R Documentation |
Partially inspired by phylosmith::tsne_phyloseq()
function developed by Schuyler D. Smith.
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,
...
)
physeq |
(required): a |
method |
A method to calculate distance using |
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 |
perplexity |
(Numeric) Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details in the man page of |
fact |
Name of the column in |
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 |
A ggplot object
Adrien Taudière
data(data_fungi)
if (requireNamespace("Rtsne")) {
plot_tsne_pq(data_fungi, fact = "Height", perplexity = 15)
}
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)
}
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