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Add taxonomic prefixes to tax_table columns

Source: R/modify_taxonomy_prefix.R
add_taxonomy_prefix.Rd

Adds QIIME-style two-underscore prefixes (e.g., "k__", "p__") to values in a taxonomy matrix or data.frame if they are not already present. The function is idempotent, meaning it will not add duplicate prefixes when reapplied.

Usage

add_taxonomy_prefix(
  me,
  prefix_map = c(Kingdom = "k__", Phylum = "p__", Class = "c__", Order = "o__", Family =
    "f__", Genus = "g__", Species = "s__", Strain = "t__")
)

Arguments

me

A character matrix, data.frame, microEDA or phyloseq-class object containing a tax_table. If a microEDA or phyloseq object is passed, its internal taxonomyTable is modified.

prefix_map

A named character vector mapping taxonomic rank names (e.g., "Kingdom", "Phylum") to their corresponding prefixes (e.g., "k__", "p__"). Defaults to standard QIIME-style prefixes for common ranks including "Strain" ("t__").

Value

Returns the input object with prefixes added to appropriate cells:

  • For matrices/data.frames: returns the modified matrix or data.frame.

  • For microEDA/phyloseq objects: returns the updated microEDA/phyloseq object with prefixed tax_table.

Details

This function supports both character matrices/data.frames and microEDA or phyloseq objects. It only modifies columns matching known taxonomic ranks (as defined in prefix_map), leaving other columns and missing/empty values (NA, "", " ") unchanged.

  • Only columns in me that match keys in prefix_map are processed.

  • Values already starting with any valid prefix (e.g., "k__Bacteria") are skipped.

  • Empty strings (""), NA, and whitespace-only entries are preserved without modification.

See also

trim_taxonomy_prefix() to remove prefixes.

tax_table() to access taxonomy data.

Examples

# Example 1: Basic usage with data.frame
tax_data <- data.frame(
  Kingdom = c("Bacteria", "Archaea"),
  Phylum = c("Proteobacteria", "Euryarchaeota"),
  Genus = c("Escherichia", "Methanobrevibacter"),
  Species = c("Escherichia coli", "Methanobrevibacter smithii"),
  stringsAsFactors = FALSE
)

prefixed <- add_taxonomy_prefix(tax_data)
prefixed
#>       Kingdom            Phylum                 Genus
#> 1 k__Bacteria p__Proteobacteria        g__Escherichia
#> 2  k__Archaea  p__Euryarchaeota g__Methanobrevibacter
#>                         Species
#> 1           s__Escherichia coli
#> 2 s__Methanobrevibacter smithii

# Example 2: Idempotent (applying again changes nothing)
add_taxonomy_prefix(prefixed)
#>       Kingdom            Phylum                 Genus
#> 1 k__Bacteria p__Proteobacteria        g__Escherichia
#> 2  k__Archaea  p__Euryarchaeota g__Methanobrevibacter
#>                         Species
#> 1           s__Escherichia coli
#> 2 s__Methanobrevibacter smithii

# Example 3: Basic usage with phyloseq objects
data("GlobalPatterns", package = "phyloseq")
GlobalPatterns <- add_taxonomy_prefix(GlobalPatterns)
head(phyloseq::tax_table(GlobalPatterns)[, c("Kingdom", "Phylum", "Order")])
#> Taxonomy Table:     [6 taxa by 3 taxonomic ranks]:
#>        Kingdom      Phylum             Order            
#> 549322 "k__Archaea" "p__Crenarchaeota" NA               
#> 522457 "k__Archaea" "p__Crenarchaeota" NA               
#> 951    "k__Archaea" "p__Crenarchaeota" "o__Sulfolobales"
#> 244423 "k__Archaea" "p__Crenarchaeota" NA               
#> 586076 "k__Archaea" "p__Crenarchaeota" NA               
#> 246140 "k__Archaea" "p__Crenarchaeota" NA