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,
  show_count = FALSE,
  facet_by = NULL,
  growing_text = TRUE,
  text_size = 15,
  show_na = TRUE,
  na_label = "NA",
  min_text_size = 0,
  ...
)

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(x + 1) transformed. The +1 ensures that taxa with a count of 1 still have a visible tile area.
plot_legend: (logical, default FALSE) If TRUE, plot che legend of color for lvl 1
show_count: (logical, default FALSE) If TRUE, appends the raw count in parentheses after each lvl2 label, e.g. "Agaricus (42)".
facet_by: (character, default NULL) Name of a column in sample_data(physeq) to facet by. Each level produces its own treemap panel via ggplot2::facet_wrap().
growing_text: (logical, default TRUE) If FALSE, all tile labels are drawn at the same font size (disables per-tile text growing), which corresponds to the smallest size that would otherwise be computed.
text_size: (numeric, default 15) Base font size for tile labels. Mostly useful when growing_text = FALSE, as it sets the size of all labels.
show_na: (logical, default TRUE) If TRUE, taxa with NA values for lvl1 or lvl2 are kept and displayed as a grey "NA" area. If FALSE, they are removed (previous default behavior).
na_label: (character, default "NA") Label used to replace NA values in lvl1 and lvl2 when show_na = TRUE.
min_text_size: (numeric, default 0) Minimum font size in points for tile labels. Labels that would be smaller than this are hidden. Set to 0 to always show all labels.
...: Additional 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
  )
  treemap_pq(
    clean_pq(subset_taxa(
      data_fungi_sp_known,
      Phylum == "Basidiomycota"
    )),
    "Order", "Class",
    show_count = TRUE, log10trans = FALSE
  )
}
#> Cleaning suppress 0 taxa and 5 samples.
#> Cleaning suppress 0 taxa and 5 samples.
#> Cleaning suppress 0 taxa and 5 samples.

# }