tax_prepend_ranks: Add rank prefixes to phyloseq tax_table values

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

Add rank prefixes to phyloseq tax_table values

Description

Prepend the start of rank names to each taxon at each rank (useful particularly in case of duplicated taxa names across ranks, e.g. dietswap dataset)

Usage

tax_prepend_ranks(ps, sep = ": ", nchar = 1)

Arguments

ps	phyloseq object
sep	characters to paste in between rank initial and taxon name
nchar	number of characters to use from start of rank_names

Value

phyloseq

See Also

tax_fix for fixing other tax_table problems

Examples

data("dietswap", package = "microbiome")
phyloseq::tax_table(dietswap) %>% head()
dietswap %>%
  tax_prepend_ranks() %>%
  phyloseq::tax_table() %>%
  head()

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