\name{otu2df}
\alias{otu2df}
\title{Convert an otuTable object into a data.frame useful for plotting
in the ggplot2 framework.}
\usage{
  otu2df(otu, taxavec, map, keepOnlyTheseTaxa=NULL,
  threshold=NULL)
}
\arguments{
  \item{otu}{An \code{otuTable} object.}

  \item{taxavec}{A character vector of the desired
  taxonomic names to categorize each species in otu.}

  \item{map}{The corresponding sampleData object for
  \code{otu}.}

  \item{keepOnlyTheseTaxa}{A vector of the taxonomic labels
  that you want included. If NULL, the default, then all
  taxonomic labels are used, except for the empty character
  string, ``'', which is trimmed away.}

  \item{threshold}{A [0,1] numeric. Fraction of abundance
  of the taxonomic groups to keep for each sample. The
  higher the value, the larger the diversity of taxonomic
  groups included. That is, a greater number of the rare
  groups are included. If NULL (or 1), the default, all
  taxonomic groups are included.}
}
\description{
  Convert an otuTable object into a data.frame useful for
  plotting in the ggplot2 framework.
}
\keyword{internal}