adding del.gaps()

[ape.git] / man / plot.cophylo.Rd

diff --git a/man/plot.cophylo.Rd b/man/plot.cophylo.Rd
index 38ce54a870dc8aa17a6876b8f0e4393fc6e87d4a..64e140d77c6a3d7692d74395835e68061c6732bc 100644 (file)
--- a/man/plot.cophylo.Rd
+++ b/man/plot.cophylo.Rd
@@ -5,11 +5,13 @@
   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{
-plot.cophylo(phy1, phy2, 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)
+plot.cophylo(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)
 }
 
 \arguments{
-  \item{phy1, phy2}{two objects of class \code{"phylo"}.}
+  \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.}
@@ -19,7 +21,10 @@ plot.cophylo(phy1, phy2, assoc=NULL, use.edge.length=FALSE,space=0, length.line=
   \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{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{
 The aim of this function is to plot simultaneously two phylogenetic trees with associated taxa. The two trees do not necessarily have the same number of tips and more than one tip in one phylogeny can be associated with a tip in the other.