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\name{plot.pvclust}
\alias{plot.pvclust}
\alias{text.pvclust}
\title{Draws Dendrogram with P-values for Pvclust Object}
\description{
plot dendrogram for a \code{pvclust} object and add \eqn{p}-values for
clusters.
}
\usage{
\method{plot}{pvclust}(x, print.pv=TRUE, print.num=TRUE, float=0.01,
col.pv=c(2,3,8), cex.pv=0.8, font.pv=NULL, col=NULL, cex=NULL,
font=NULL, lty=NULL, lwd=NULL, main=NULL, sub=NULL, xlab=NULL, ...)
\method{text}{pvclust}(x, col=c(2,3,8), print.num=TRUE, float=0.01, cex=NULL, font=NULL, ...)
}
\arguments{
\item{x}{object of class \code{pvclust}, which is generated by
function \code{pvclust}. See \code{\link{pvclust}} for details.}
\item{print.pv}{logical flag to specify whether print \eqn{p}-values
above the edges (clusters).}
\item{print.num}{logical flag to specify whether print edge numbers
below clusters.}
\item{float}{numeric value to adjust the height of \eqn{p}-values from
edges.}
\item{col.pv}{numeric vector of length three to specify the colors for
\eqn{p}-values and edge numbers. From the beginning each value
corresponds to the color of AU values, BP values and edge numbers,
respectively.}
\item{cex.pv}{numeric value which specifies the size of characters for
\eqn{p}-values and edge numbers. See \code{cex} argument for
\code{\link[graphics]{par}}.}
\item{font.pv}{numeric value which specifies the font of characters
for \eqn{p}-values and edge numbers. See \code{font} argument for
\code{\link[graphics]{par}}.}
\item{col, cex, font}{in \code{text} function, they correspond to
\code{col.pv}, \code{cex.pv} and \code{font.pv} in \code{plot}
function, respectively. In \code{plot} function they are used as
generic graphic parameters.}
\item{lty, lwd, main, sub, xlab, ...}{
generic graphic parameters. See \code{\link[graphics]{par}} for
details.}
}
\details{
This function plots a dendrogram with \eqn{p}-values for given object
of class \code{pvclust}. AU \eqn{p}-value (printed in red color in
default) is the abbreviation of "approximately unbiased"
\eqn{p}-value, which is calculated by multiscale bootstrap
resampling. BP value (printed in green color in default) is "bootstrap
probability" value, which is less accurate than AU value as
\eqn{p}-value. One can consider that clusters (edges) with high AU
values (e.g. 95\%) are strongly supported by data.
}
\seealso{\code{\link{text.pvclust}}}
\references{
Shimodaira, H. (2004)
"Approximately unbiased tests of regions using multistep-multiscale
bootstrap resampling",
\emph{Annals of Statistics}, 32, 2616-2641.
Shimodaira, H. (2002)
"An approximately unbiased test of phylogenetic tree selection",
\emph{Systematic Biology}, 51, 492-508.
}
\author{Ryota Suzuki \email{suzuki@ef-prime.com}}
\keyword{hplot}
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