% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/internals.R
\name{amp_rename}
\alias{amp_rename}
\title{Tidy up taxonomy}
\usage{
amp_rename(data, tax_class = NULL, tax_empty = "best", tax_level = "Genus")
}
\arguments{
\item{data}{(\emph{required}) Data list as loaded with \code{\link{amp_load}}.}

\item{tax_class}{Converts a specific phylum to class level instead, e.g. \code{"p__Proteobacteria"}.}

\item{tax_empty}{How to show OTUs without taxonomic information. One of the following:
\itemize{
   \item \code{"remove"}: Remove OTUs without taxonomic information.
   \item \code{"best"}: (\emph{default}) Use the best classification possible.
   \item \code{"OTU"}: Display the OTU name.
   }}

\item{tax_level}{The taxonomic level to remove OTUs with no assigned taxonomy, only used when \code{tax_empty = "remove"}. (\emph{default:} \code{"Genus"})}
}
\value{
A list with 3 dataframes (4 if reference sequences are provided).
}
\description{
Used internally in other ampvis functions.
}
\author{
Kasper Skytte Andersen \email{ksa@bio.aau.dk}

Mads Albertsen \email{MadsAlbertsen85@gmail.com}
}
\keyword{internal}
