Ridges plot of sample distribution across taxa

Graphical representation of distribution of samples across taxa using ridges. This is the sample-centric counterpart of ridges_pq(): each ridge represents a taxon (at tax_level) and the x-axis shows the abundance distribution across samples, optionally colored by a sample factor.

Usage

ridges_sam_pq(
  physeq,
  fact,
  nb_seq = TRUE,
  log10trans = TRUE,
  tax_level = "Class",
  type = "density",
  ...
)

Arguments

physeq

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

fact

(required) Name of the factor in physeq@sam_data used to color the ridges

nb_seq

(logical; default TRUE) If set to FALSE, only the number of samples is counted. Concretely, physeq otu_table is transformed in a binary otu_table (each value different from zero is set to one)

log10trans

(logical, default TRUE) If TRUE, the abundance is log10 transformed.

tax_level

The taxonomic level used for grouping taxa on the y-axis

type

Either "density" (the default) or "ecdf" to plot a cumulative version using ggplot2::stat_ecdf()

...

Other params passed on to ggridges::geom_density_ridges()

Value

A ggplot2 plot with ridges representing the distribution of samples for each taxon

Author

Adrien Taudière

Examples

if (requireNamespace("ggridges")) {
  ridges_sam_pq(data_fungi_mini, "Height", alpha = 0.5,
    log10trans = FALSE, tax_level = "Genus") +
  xlim(c(0, 1000))
}
#> Loading required namespace: ggridges
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Picking joint bandwidth of 36.4
#> Warning: Removed 99 rows containing non-finite outside the scale range
#> (`stat_density_ridges()`).

# \donttest{
if (requireNamespace("ggridges")) {
  ridges_sam_pq(data_fungi_mini, "Height", alpha = 0.5, scale = 0.9)
  ridges_sam_pq(data_fungi_mini, "Height",
    alpha = 0.5, scale = 0.9,
    type = "ecdf"
  )
}

# }