new option 'rotate.tree' in plot.phylo()

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

diff --git a/man/plot.phylo.Rd b/man/plot.phylo.Rd
index ba98021ef7374fc5ee5199024f47960293b3210d..f19db415317559caa2c338cf9d3b677b6ad6d3db 100644 (file)
--- a/man/plot.phylo.Rd
+++ b/man/plot.phylo.Rd
@@ -9,7 +9,8 @@
     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{
@@ -90,9 +91,15 @@
     \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
@@ -160,12 +167,12 @@
   \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)