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Remove taxonomic prefixes from tax_table columns

Source: R/modify_taxonomy_prefix.R
trim_taxonomy_prefix.Rd

Removes QIIME-style two-underscore prefixes (e.g., "k__", "p__") from values in a taxonomy matrix or data.frame if present. The function is idempotent: repeated application has no additional effect.

Usage

trim_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 a phyloseq-class object containing a tax_table. If a microEDA or phyloseq object is passed, its 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 including "Strain" ("t__").

Value

Returns the input object with prefixes removed:

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

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

Details

Supports character matrices, data.frames, microEDA and phyloseq objects. Only modifies cells in columns matching the keys of prefix_map and only when the value starts with the corresponding prefix. Missing (NA), empty, or unprefixed values are left unchanged.

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

  • Prefix removal is exact: e.g., "k__" is only removed from "Kingdom" column if it starts the value.

  • Uses efficient string processing (e.g., via stringi) to detect and remove prefixes.

  • Preserves NA, "", and whitespace-only entries.

See also

add_taxonomy_prefix() to add prefixes.

tax_table() to access taxonomy data.

Examples

# Example 1: Basic usage with data.frame
prefixed_tax_data <- data.frame(
  Kingdom = c("k__Bacteria", "k__Archaea"),
  Genus = c("g__Escherichia", "g__Methanobrevibacter"),
  Species = c("s__Escherichia coli", "s__Methanobrevibacter smithii"),
  stringsAsFactors = FALSE
)
prefixed_tax_data
#>       Kingdom                 Genus                       Species
#> 1 k__Bacteria        g__Escherichia           s__Escherichia coli
#> 2  k__Archaea g__Methanobrevibacter s__Methanobrevibacter smithii
trimmed <- trim_taxonomy_prefix(prefixed_tax_data)
trimmed
#>    Kingdom              Genus                    Species
#> 1 Bacteria        Escherichia           Escherichia coli
#> 2  Archaea Methanobrevibacter Methanobrevibacter smithii

# Example 2: Idempotent (applying again changes nothing)
trim_taxonomy_prefix(trimmed)
#>    Kingdom              Genus                    Species
#> 1 Bacteria        Escherichia           Escherichia coli
#> 2  Archaea Methanobrevibacter 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               

GlobalPatterns <- trim_taxonomy_prefix(GlobalPatterns)
head(phyloseq::tax_table(GlobalPatterns)[, c("Kingdom", "Phylum", "Order")])
#> Taxonomy Table:     [6 taxa by 3 taxonomic ranks]:
#>        Kingdom   Phylum          Order         
#> 549322 "Archaea" "Crenarchaeota" NA            
#> 522457 "Archaea" "Crenarchaeota" NA            
#> 951    "Archaea" "Crenarchaeota" "Sulfolobales"
#> 244423 "Archaea" "Crenarchaeota" NA            
#> 586076 "Archaea" "Crenarchaeota" NA            
#> 246140 "Archaea" "Crenarchaeota" NA