tax_name: Simple way to set unique taxa_names for phyloseq object

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Simple way to set unique taxa_names for phyloseq object

Description

If your current taxa_names aren't what you want (e.g. they are long DNA sequences), this function will help you set sensible unique names.

It combines:

• a prefix like tax, asv, or otu (pick an appropriate prefix or set your own)

• a unique (sequential) number

• classification information from a chosen taxonomic rank (optional)

Usage

tax_name(
  ps,
  prefix = c("tax", "asv", "otu")[1],
  rank = NA,
  pad_number = TRUE,
  sep = "_"
)

Arguments

ps	phyloseq object
prefix	e.g. 'tax', 'asv', or 'otu' (or set your own)
rank	name of taxonomic rank from which to use classifications in new names
pad_number	should unique numbers have zeros added to the front (e.g. 001, 002) to be made the same number of characters?
sep	character to separate the unique number and any taxonomic classification info (relevant if rank given)

Details

Don't confuse this with the phyloseq function taxa_names() or the newer microViz function tax_rename().

Value

phyloseq object

See Also

tax_rename for a more informative taxon naming tool

phyloseq::taxa_names for accessing and manually setting names

Examples

library(phyloseq)
# get example data
data("enterotype")
ps <- enterotype
head(taxa_names(ps)) # these are mostly fine (except the -1), but imagine you wanted new names

# consider storing the original names for reference (e.g. if they are DNA sequences)
old_taxa_names <- taxa_names(ps)

ps <- tax_name(ps)
taxa_names(ps) %>% head()

# probably better to include the genus info to make these names more informative
ps <- tax_name(ps, rank = "Genus")
taxa_names(ps) %>% head()

# store new names with old names in dataframe for reference
names_df <- tibble::tibble(old = old_taxa_names, new = taxa_names(ps))

# alternative settings
tax_name(ps, pad_number = FALSE) %>%
  taxa_names() %>%
  head()
tax_name(ps, prefix = "whateveryoulike") %>%
  taxa_names() %>%
  head()
tax_name(ps, rank = "Genus", sep = "-") %>%
  taxa_names() %>%
  head()

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.