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Rename names of ranks in the tax_table slot of a phyloseq object

Source: R/taxtab_modification.R
rename_ranks_pq.Rd

lifecycle-experimental

The users can use the function using a couple of vector old_names/new_names or using a pattern to replace by replacement

Usage

rename_ranks_pq(
  physeq,
  old_names = NULL,
  new_names = NULL,
  pattern = NULL,
  replacement = NULL,
  fixed = FALSE,
  perl = FALSE,
  useBytes = FALSE
)

Arguments

physeq

(required) A phyloseq object.

old_names

(character vector, default NULL) Names of the columns to replace.

new_names

(character vector, default NULL) New names for the columns.

pattern

(character, default NULL) Pattern to replace by the replacement argument.

replacement

(character, default NULL) Replacement string for the pattern.

fixed

(logical, default FALSE) See ?grep.

perl

(logical, default FALSE) See ?grep.

useBytes

(logical, default FALSE) See ?grep.

Value

An object of class phyloseq

Author

Adrien Taudière

Examples

rename_ranks_pq(data_fungi, c("Confidence.Ranking", "Phylum"), c("Conf.Rank.Guild", "Phyla"))@tax_table |>
  colnames()
#>  [1] "Domain"          "Phyla"           "Class"           "Order"          
#>  [5] "Family"          "Genus"           "Species"         "Trophic.Mode"   
#>  [9] "Guild"           "Trait"           "Conf.Rank.Guild" "Genus_species"  
rename_ranks_pq(data_fungi, pattern = ".", replacement = "_", fixed = TRUE)@tax_table |>
  colnames()
#>  [1] "Domain"             "Phylum"             "Class"             
#>  [4] "Order"              "Family"             "Genus"             
#>  [7] "Species"            "Trophic_Mode"       "Guild"             
#> [10] "Trait"              "Confidence_Ranking" "Genus_species"