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Shorten clade names in a dataset to chosen taxonomic level

Source: R/clean_names.R
shorten_clade_names.Rd

This function shortens the taxonomic names of clades in a given dataset based on a specified taxonomic level, using the first letter of the taxonomic rank + "__" as rank identifiers.

Usage

shorten_clade_names(
  data,
  taxa_lvl,
  apply_to_colnames = TRUE,
  selected_cols = NULL
)

Arguments

data

The input dataset. Assumes clade names are of the structure k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae and found in the 'clade_name' column or the column names themselves.

taxa_lvl

The taxonomic level at which the clade names should be shortened. Valid options include 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species' or 't' (SGB). First letter abbreviations (e.g., 's') are also accepted.

apply_to_colnames

Logical indicating whether the shortening should be applied to column names or row values. Default is TRUE.

selected_cols

A character vector specifying the columns to which the shortening should be applied. If NULL (the default), the shortening is applied to all columns.

Value

The dataset with the clade names shortened based on the specified taxonomic level.

In the case where there are entries not matching the chosen taxonomic rank, these are either returned 'as is', or if they follow the same structure, the name will be shortened to the last taxonomic entry (see rows 2, 5 and 6 of the example)

Note

This function is not intended to be used with the workflow for the creation of phyloseq objects as the full sequence of taxonomic names is needed for the creation of the taxonomy table in get_taxa_table(). It may however be useful for analyses or plots created directly with/from the dataframes.

This function uses the dplyr package for data manipulation.

Author

Jérémy Rotzetter

Examples

head(merged_abundance_profiles$clade_name)
#> [1] "UNCLASSIFIED"                                        
#> [2] "k__Bacteria"                                         
#> [3] "k__Bacteria|p__Proteobacteria"                       
#> [4] "k__Bacteria|p__Actinobacteria"                       
#> [5] "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria"
#> [6] "k__Bacteria|p__Actinobacteria|c__Actinomycetia"      

taxa_shortened <- shorten_clade_names(
  merged_abundance_profiles,
  "Phylum",
  apply_to_colnames = FALSE,
  selected_cols = "clade_name"
)

head(taxa_shortened$clade_name)
#> [1] "UNCLASSIFIED"           "k__Bacteria"            "Proteobacteria"        
#> [4] "Actinobacteria"         "c__Gammaproteobacteria" "c__Actinomycetia"