\usage{
\method{plot}{phylo}(x, type = "phylogram", use.edge.length = TRUE,
node.pos = NULL, show.tip.label = TRUE, show.node.label = FALSE,
- edge.color = "black", edge.width = 1, font = 3,
+ edge.color = "black", edge.width = 1, edge.lty = 1, font = 3,
cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE,
root.edge = FALSE, label.offset = 0, underscore = FALSE,
x.lim = NULL, y.lim = NULL, direction = "rightwards",
- lab4ut = "horizontal", tip.color = "black", ...)
+ lab4ut = "horizontal", tip.color = "black", plot = TRUE,
+ rotate.tree = 0, ...)
\method{plot}{multiPhylo}(x, layout = 1, ...)
}
\arguments{
the plotted phylogeny. These are taken to be in the same order than
the component \code{edge} of \code{phy}. If fewer widths are given
than the length of \code{edge}, then these are recycled.}
+ \item{edge.lty}{same than the previous argument but for line types;
+ 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash.}
\item{font}{an integer specifying the type of font for the labels: 1
(plain text), 2 (bold), 3 (italic, the default), or 4 (bold
italic).}
\code{type = "unrooted"}.}
\item{tip.color}{the colours used for the tip labels, eventually
recycled (see examples).}
+ \item{plot}{a logical controlling whether to draw the tree. If
+ \code{FALSE}, the graphical device is set as if the tree was
+ plotted, and the coordinates are saved as well.}
\item{layout}{the number of trees to be plotted simultaneously.}
- \item{...}{further arguments to be passed to \code{plot} or to
+ \item{\dots}{further arguments to be passed to \code{plot} or to
\code{plot.phylo}.}
+ \item{rotate.tree}{for "fan", "unrooted", or "radial" trees: the
+ rotation of the whole tree in degrees (negative values are
+ accepted).}
}
\description{
These functions plot phylogenetic trees on the current graphical
\item{Ntip}{}
\item{Nnode}{}
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
- \code{\link{read.tree}}, \code{\link{add.scale.bar}},
- \code{\link{axisPhylo}}, \code{\link{nodelabels}},
- \code{\link[graphics]{plot}} for the basic
- plotting function in R
+ \code{\link{read.tree}}, \code{\link{trex}}, \code{\link{kronoviz}},
+ \code{\link{add.scale.bar}}, \code{\link{axisPhylo}},
+ \code{\link{nodelabels}}, \code{\link{edges}},
+ \code{\link[graphics]{plot}} for the basic plotting function in R
}
\examples{
### An extract from Sibley and Ahlquist (1990)