Ridge plot of a phyloseq object — ridges

Graphical representation of distribution of taxa across a factor using ridges.

Usage

ridges_pq(
  physeq,
  fact,
  nb_seq = TRUE,
  log10trans = TRUE,
  tax_level = "Class",
  ...
)

Arguments

physeq: (required): a phyloseq-class object obtained using the phyloseq package.
fact: (required) Name of the factor in physeq@sam_data used to plot different lines
nb_seq: (logical; default TRUE) If set to FALSE, only the number of ASV is count. 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 number of sequences (or ASV if nb_seq = FALSE) is log10 transformed.
tax_level: The taxonomic level to fill ridges
...: Other params passed on to ggridges::geom_density_ridges()

Value

A ggplot2 plot with bar representing the number of sequence en each taxonomic groups

Author

Adrien Taudière

Examples

if (requireNamespace("ggridges")) {
  ridges_pq(data_fungi_mini, "Time", alpha = 0.5, log10trans = FALSE) + 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 40.1
#> Warning: Removed 99 rows containing non-finite outside the scale range
#> (`stat_density_ridges()`).

# \donttest{
if (requireNamespace("ggridges")) {
  ridges_pq(data_fungi_mini, "Time", alpha = 0.5, scale = 0.9)
  ridges_pq(data_fungi_mini, "Sample_names", log10trans = TRUE) + facet_wrap("~Height")

  ridges_pq(data_fungi_mini,
    "Time",
    jittered_points = TRUE,
    position = ggridges::position_points_jitter(width = 0.05, height = 0),
    point_shape = "|", point_size = 3, point_alpha = 1, alpha = 0.7,
    scale = 0.8
  )
}
#> Picking joint bandwidth of 0.428

# }