Select taxonomic ranks in a phyloseq object — select_ranks

Useful in tidyverse-like pipeline.

Usage

select_ranks_pq(physeq, ...)

Arguments

physeq: (required) A phyloseq object.
...: One or more unquoted expressions separated by commas. Variable names can be used as if they were positions in the data frame, so expressions like x:y can be used to select a range of variables. See ?dplyr::select.

Value

A phyloseq object

Author

Adrien Taudière

Examples

select_ranks_pq(data_fungi, Order, Family)@tax_table |>
  dim()
#> [1] 1420    2
select_ranks_pq(data_fungi, !Order)@tax_table |>
  colnames()
#>  [1] "Domain"             "Phylum"             "Class"             
#>  [4] "Family"             "Genus"              "Species"           
#>  [7] "Trophic.Mode"       "Guild"              "Trait"             
#> [10] "Confidence.Ranking" "Genus_species"     
#