Plot treemap of 2 taxonomic levels — treemap

Note that lvl2need to be nested in lvl1

Usage

treemap_pq(
  physeq,
  lvl1,
  lvl2,
  nb_seq = TRUE,
  log10trans = TRUE,
  plot_legend = FALSE,
  ...
)

Arguments

physeq: (required): a phyloseq-class object obtained using the phyloseq package.
lvl1: (required) Name of the first (higher) taxonomic rank of interest
lvl2: (required) Name of the second (lower) taxonomic rank of interest
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.
plot_legend: (logical, default FALSE) If TRUE, plot che legend of color for lvl 1
...: Other arguments passed on to treemapify::geom_treemap() function.

Value

A ggplot2 object

Author

Adrien Taudière

Examples

data(data_fungi_sp_known)
if (requireNamespace("treemapify")) {
  treemap_pq(
    clean_pq(subset_taxa(
      data_fungi_sp_known,
      Phylum == "Basidiomycota"
    )),
    "Order", "Class",
    plot_legend = TRUE
  )
}
#> Loading required namespace: treemapify
#> Cleaning suppress 0 taxa and 5 samples.

# \donttest{
if (requireNamespace("treemapify")) {
  treemap_pq(
    clean_pq(subset_taxa(
      data_fungi_sp_known,
      Phylum == "Basidiomycota"
    )),
    "Order", "Class",
    log10trans = FALSE
  )
  treemap_pq(
    clean_pq(subset_taxa(
      data_fungi_sp_known,
      Phylum == "Basidiomycota"
    )),
    "Order", "Class",
    nb_seq = FALSE, log10trans = FALSE
  )
}
#> Cleaning suppress 0 taxa and 5 samples.
#> Cleaning suppress 0 taxa and 5 samples.

# }