\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",
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).}
\item{tip.color}{the colours used for the tip labels, eventually
recycled (see examples).}
\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}.}
}
\description{
\code{plot.phylo} returns invisibly a list with the following
components which values are those used for the current plot:
- \item{type}
- \item{use.edge.length}
- \item{node.pos}
- \item{show.tip.label}
- \item{show.node.label}
- \item{font}
- \item{cex}
- \item{adj}
- \item{srt}
- \item{no.margin}
- \item{label.offset}
- \item{x.lim}
- \item{y.lim}
- \item{direction}
- \item{tip.color}
- \item{Ntip}
- \item{Nnode}
+ \item{type}{}
+ \item{use.edge.length}{}
+ \item{node.pos}{}
+ \item{show.tip.label}{}
+ \item{show.node.label}{}
+ \item{font}{}
+ \item{cex}{}
+ \item{adj}{}
+ \item{srt}{}
+ \item{no.margin}{}
+ \item{label.offset}{}
+ \item{x.lim}{}
+ \item{y.lim}{}
+ \item{direction}{}
+ \item{tip.color}{}
+ \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
+ \code{\link{edges}}, \code{\link[graphics]{plot}} for the basic
plotting function in R
}
\examples{
plot(tree.owls, type = "u", use.edge.length = FALSE)
layout(matrix(1))
-data(xenarthra)
-plot(xenarthra)
-### remove the margins...
-plot(xenarthra, no.margin = TRUE)
-### ... and use a smaller font size
-plot(xenarthra, no.margin = TRUE, cex = 0.8)
-plot(xenarthra, type = "c", no.margin = TRUE,
- use.edge.length = FALSE, cex = 0.8)
-par(mar = c(5.1, 4.1, 4.1, 2.1))
-
data(bird.orders)
### using random colours and thickness
plot(bird.orders,