This function plots two trees face to face with the links if specified. It is possible to rotate the branches of each tree around the nodes by clicking.
}
\usage{
-cophyloplot(x, y, assoc=NULL, use.edge.length=FALSE,space=0,
- length.line=1, gap=2, type="phylogram", rotate=FALSE,
- col="red", show.tip.label=TRUE, font=3, \dots)
+cophyloplot(x, y, assoc = NULL, use.edge.length = FALSE, space = 0,
+ length.line = 1, gap = 2, type = "phylogram", rotate = FALSE,
+ col = par("fg"), lwd = par("lwd"), lty = par("lty"),
+ show.tip.label = TRUE, font = 3, \dots)
}
\arguments{
\item{x, y}{two objects of class \code{"phylo"}.}
- \item{assoc}{a matrix with 2 columns specifying the associations between the tips. If NULL, no links will be drawn.}
- \item{use.edge.length}{a logical indicating whether the branch lengths should be used to plot the trees; default is FALSE.}
- \item{space}{a positive value that specifies the distance between the two trees.}
- \item{length.line}{a positive value that specifies the length of the horizontal line associated to each taxa. Default is 1.}
- \item{gap}{a value specifying the distance between the tips of the phylogeny and the lines.}
- \item{type}{a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default) or "cladogram".}
- \item{rotate}{a logical indicating whether the nodes of the phylogeny can be rotated by clicking. Default is FALSE.}
- \item{col}{a character string indicating the color to be used for the links. Default is red.}
- \item{show.tip.label}{a logical indicating whether to show the tip labels on the phylogeny (defaults to 'TRUE', i.e. the labels are shown).}
- \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{assoc}{a matrix with 2 columns specifying the associations
+ between the tips. If NULL, no links will be drawn.}
+ \item{use.edge.length}{a logical indicating whether the branch lengths
+ should be used to plot the trees; default is FALSE.}
+ \item{space}{a positive value that specifies the distance between the
+ two trees.}
+ \item{length.line}{a positive value that specifies the length of the
+ horizontal line associated to each taxa. Default is 1.}
+ \item{gap}{a value specifying the distance between the tips of the
+ phylogeny and the lines.}
+ \item{type}{a character string specifying the type of phylogeny to be
+ drawn; it must be one of "phylogram" (the default) or "cladogram".}
+ \item{rotate}{a logical indicating whether the nodes of the phylogeny
+ can be rotated by clicking. Default is FALSE.}
+ \item{col}{a character vector indicating the color to be used for the
+ links; recycled as necessary.}
+ \item{lwd}{id. for the width.}
+ \item{lty}{id. for the line type.}
+ \item{show.tip.label}{a logical indicating whether to show the tip
+ labels on the phylogeny (defaults to 'TRUE', i.e. the labels are
+ shown).}
+ \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{\dots}{(unused)}
}
\details{