X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fplot.phylo.Rd;h=6d08946052aa33925df254d2116ccb35f729c204;hb=a2fc961dffe9f9b7994ed880e68c03b2334dc341;hp=8ac1519c7a198c22257cbae831c28f1626932e10;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git

diff --git a/man/plot.phylo.Rd b/man/plot.phylo.Rd
index 8ac1519..6d08946 100644
--- a/man/plot.phylo.Rd
+++ b/man/plot.phylo.Rd
@@ -5,11 +5,12 @@
 \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, open.angle = 0, ...)
 \method{plot}{multiPhylo}(x, layout = 1, ...)
 }
 \arguments{
@@ -42,6 +43,8 @@
     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).}
@@ -88,9 +91,18 @@
     \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{rotate.tree}{for "fan", "unrooted", or "radial" trees: the
+    rotation of the whole tree in degrees (negative values are
+    accepted).}
   \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{open.angle}{if \code{type = "f"}, the angle in degrees left
+    blank. Use a non-zero value if you want to call
+    \code{\link{axisPhylo}} after the tree is plotted.}
 }
 \description{
   These functions plot phylogenetic trees on the current graphical
@@ -102,8 +114,7 @@
   \code{...} and could be any one of those listed above for a single
   tree.
 
-  The formatting of the labels of both the nodes and the tips is the
-  same.
+  The font format of the labels of the nodes and the tips is the same.
 
   If \code{no.margin = TRUE}, the margins are set to zero and are not
   restored after plotting the tree, so that the user can access the
@@ -131,37 +142,40 @@
   give a nice result: the user may check these values with the
   (invisibly) returned list (see ``Value:'').
 
-  Note that if you resize manually the graphical device (windows or X11)
-  you may need to replot the tree.
+  If you resize manually the graphical device (windows or X11) you may
+  need to replot the tree.
+}
+\note{
+  The argument \code{asp} cannot be passed with \code{\dots}.
 }
 \value{
   \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
-  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)
@@ -182,16 +196,6 @@ plot(tree.owls, type = "c", use.edge.length = FALSE)
 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,