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Convert a tax_table into a data.frame with numeric and list columns

Source: R/tax_table_to_df.R
tax_table_to_df.Rd

lifecycle-experimental

The tax_table slot of a phyloseq object is stored as a character matrix, so numeric information (e.g. a bootstrap support, a trait value) is silently coerced to text and list-valued cells cannot be represented at all. This helper lifts those limitations by returning a tibble in which columns that look numeric (or logical) are converted to their natural type, and selected columns can be split into genuine list columns.

It does not modify the phyloseq object; it produces a stand-alone tibble for downstream (tidyverse) manipulation.

Usage

tax_table_to_df(
  physeq,
  convert = TRUE,
  split = NULL,
  sep = "/",
  taxa_names_col = "taxon"
)

Arguments

physeq

(phyloseq or taxonomyTable, required) A phyloseq object with a tax_table slot, or a tax_table object directly.

convert

(logical, default TRUE) If TRUE, each column is passed through utils::type.convert() (with as.is = TRUE) so that columns holding only numbers become numeric/integer and "TRUE"/"FALSE" columns become logical. Columns with any non-numeric value are kept as character.

split

(character, optional) Names of columns to turn into list columns by splitting each cell on sep. Useful when a rank cell packs several values (e.g. multiple GBIF matches).

sep

(character, default "/") Separator used to split the columns named in split. Passed to base::strsplit() with fixed = TRUE.

taxa_names_col

(character or NULL, default "taxon") Name of the leading column holding the taxa names. If NULL, taxa names are kept as row names instead of a column.

Value

A tibble::tibble with one row per taxon and one column per taxonomic rank, plus (unless taxa_names_col is NULL) a leading column of taxa names.

See also

phyloseq::tax_table()

Author

Adrien Taudière

Examples

data_fungi_mini <-
 tidypq::mutate_taxa_pq(data_fungi_mini,
 Mol_Abundance = taxa_sums(.))

# Numeric-looking ranks are converted to numeric
df <- tax_table_to_df(data_fungi_mini)
df |>
  group_by(Class) |>
  summarize(mean=mean(Mol_Abundance))
#> # A tibble: 4 × 2
#>   Class                mean
#>   <chr>               <dbl>
#> 1 Agaricomycetes     13105.
#> 2 Atractiellomycetes 11053 
#> 3 Tremellomycetes     7750.
#> 4 NA                  5675 


if (FALSE) { # \dontrun{
# Split a packed column into a list column
  tax_table_to_df(data_fungi_mini, split = "Genus", sep = "_")
} # }