label_duplicate_taxa: Add unique labels to identical taxa

In gmteunisse/Fantaxtic: Fantaxtic - nested bar plots for phyloseq data

Add unique labels to identical taxa

Description

This function takes a phyloseq object and adds a label (<id>) to ASVs with the same taxonomic annotation (<tax>). The label is either the ASV name (taken from row.names) or the count of each duplicated taxon.

Usage

label_duplicate_taxa(
  ps_obj,
  tax_level,
  asv_as_id = F,
  duplicate_label = "<tax> <id>"
)

Arguments

ps_obj	Phyloseq object
tax_level	The taxonomic level at which to identify duplicates.
asv_as_id	use ASVs as ids, rather than counts?
duplicate_label	String that specifies how to construct the label. Must contain at least <tax> and <id>

Value

A phyloseq object

gmteunisse/Fantaxtic documentation built on June 7, 2024, 8:47 a.m.