Computes a manifold approximation and projection (UMAP) for phyloseq object

https://journals.asm.org/doi/full/10.1128/msystems.00691-21

Usage

umap_pq(physeq, pkg = "umap", ...)

Arguments

physeq

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

pkg

Which R packages to use, either "umap" or "uwot".

...

Additional arguments passed on to umap::umap() or uwot::umap2() function. For example n_neighbors set the number of nearest neighbors (Default 15). See umap::umap.defaults() or uwot::umap2() for the list of parameters and default values.

Value

A dataframe with samples informations and the x_umap and y_umap position

Details

This function is mainly a wrapper of the work of others. Please make a reference to umap::umap() if you use this function.

See also

umap::umap(), tsne_pq(), phyloseq::plot_ordination()

Author

Adrien Taudière

Examples

library("umap")
data_f <- prune_samples(
  sample_names(data_fungi_mini)[1:20],
  data_fungi_mini
)
df_umap <- umap_pq(data_f, n_neighbors = 3)
#> Taxa are now in columns.
#> Taxa are now in rows.
#> Joining with `by = join_by(Sample)`
#> Joining with `by = join_by(Sample)`
ggplot(df_umap, aes(x = x_umap, y = y_umap, col = Height)) +
  geom_point(size = 2)


if (FALSE) { # \dontrun{
df_uwot <- umap_pq(data_fungi_mini, pkg = "uwot")
library(patchwork)
physeq <- data_fungi_mini
df_umap <- umap_pq(physeq, n_neighbors = 3)
res_tsne <- tsne_pq(data_fungi_mini)
df_umap_tsne <- df_umap
df_umap_tsne$x_tsne <- res_tsne$Y[, 1]
df_umap_tsne$y_tsne <- res_tsne$Y[, 2]
((ggplot(df_umap, aes(x = x_umap, y = y_umap, col = Height)) +
  geom_point(size = 2) +
  ggtitle("UMAP")) +
  (plot_ordination(physeq,
    ordination = ordinate(physeq, method = "PCoA", distance = "bray"),
    color = "Height"
  ) + ggtitle("PCoA"))) /
  ((ggplot(df_umap_tsne, aes(x = x_tsne, y = y_tsne, col = Height)) +
    geom_point(size = 2) +
    ggtitle("tsne")) +
    (plot_ordination(physeq,
      ordination = ordinate(physeq, method = "NMDS", distance = "bray"),
      color = "Height"
    ) + ggtitle("NMDS"))) +
  patchwork::plot_layout(guides = "collect")

(ggplot(df_umap, aes(x = x_umap, y = y_umap, col = Height)) +
  geom_point(size = 2) +
  ggtitle("umap::umap")) /
  (ggplot(df_uwot, aes(x = x_umap, y = y_umap, col = Height)) +
    geom_point(size = 2) +
    ggtitle("uwot::umap2"))
} # }