treemap_pq: Plot treemap of 2 taxonomic levels

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Plot treemap of 2 taxonomic levels

Description

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 graphic

Author(s)

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
  )
}

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
  )
}

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.