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\name{plotTreeTime}
\alias{plotTreeTime}
\title{Plot Tree With Time Axis}
\description{
This function plots a non-ultrametric tree where the tips are not
contemporary together with their dates on the x-axis.
}
\usage{
plotTreeTime(phy, tip.dates, show.tip.label = FALSE, y.lim = NULL,
color = TRUE, ...)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{tip.dates}{a vector of the same length than the number of tips
in \code{phy} (see details).}
\item{show.tip.label}{a logical value; see \code{\link{plot.phylo}}.}
\item{y.lim}{by default, one fifth of the plot is left below the tree;
use this option to change this behaviour.}
\item{color}{a logical value specifying whether to use colors for the
lines linking the tips to the time axis. If \code{FALSE}, a grey
scale is used.}
\item{\dots}{other arguments to be passed to \code{plot.phylo}.}
}
\details{
The vector \code{tip.dates} may be numeric or of class
\dQuote{\link[base]{Date}}. In either case, the time axis is set
accordingly. The length of this vector must be equal to the number of
tips of the tree: the dates are matched to the tips numbers. Missing
values are allowed.
}
\value{NULL}
\author{Emmanuel Paradis}
\seealso{
\code{\link{plot.phylo}}, \code{\link{estimate.dates}}
}
\examples{
dates <- as.Date(.leap.seconds)
tr <- rtree(length(dates))
plotTreeTime(tr, dates)
## handling NA's:
dates[11:26] <- NA
plotTreeTime(tr, dates)
## dates can be on an arbitrary scale, e.g., [-1, 1]:
plotTreeTime(tr, runif(Ntip(tr), -1, 1))
}
\keyword{hplot}
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