amp_rename: Tidy up taxonomy

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Tidy up taxonomy

Description

Used internally in other ampvis functions.

Usage

amp_rename(data, tax_class = NULL, tax_empty = "best", tax_level = "Genus")

Arguments

data	(required) Data list as loaded with amp_load.
tax_class	Converts a specific phylum to class level instead, e.g. "p__Proteobacteria".
tax_empty	How to show OTUs without taxonomic information. One of the following: "remove": Remove OTUs without taxonomic information. "best": (default) Use the best classification possible. "OTU": Display the OTU name.
tax_level	The taxonomic level to remove OTUs with no assigned taxonomy, only used when tax_empty = "remove". (default: "Genus")

Value

A list with 3 dataframes (4 if reference sequences are provided).

Author(s)

Kasper Skytte Andersen [e-mail]

Mads Albertsen [e-mail]

MadsAlbertsen/ampvis2 documentation built on Jan. 28, 2024, 7:12 a.m.