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".

...

Others 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")
df_umap <- umap_pq(data_fungi_mini)
#> Taxa are now in columns.
#> Taxa are now in rows.
#> Joining with `by = join_by(Sample)`
#> Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if
#> `.name_repair` is omitted as of tibble 2.0.0.
#> ℹ Using compatibility `.name_repair`.
#> ℹ The deprecated feature was likely used in the MiscMetabar package.
#>   Please report the issue at
#>   <https://github.com/adrientaudiere/MiscMetabar/issues>.
#> Joining with `by = join_by(Sample)`
ggplot(df_umap, aes(x = x_umap, y = y_umap, col = Height)) +
  geom_point(size = 2)


# library(patchwork)
# physeq <- data_fungi_mini
# 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")

df_uwot <- umap_pq(data_fungi_mini, pkg = "uwot")
#> 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) +
  ggtitle("umap::umap")) /
  (ggplot(df_uwot, aes(x = x_umap, y = y_umap, col = Height)) +
    geom_point(size = 2) +
    ggtitle("uwot::umap2"))