various bug fixes

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

diff --git a/man/plot.phylo.Rd b/man/plot.phylo.Rd
index b525dcc0b8cbcdc82732d3a2d0981c9b87ce8892..614ce6285a24f8f5b28209d737ddfc65c016b014 100644 (file)
--- a/man/plot.phylo.Rd
+++ b/man/plot.phylo.Rd
@@ -5,7 +5,7 @@
 \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",
@@ -42,6 +42,8 @@
     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).}
@@ -89,7 +91,7 @@
   \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{
@@ -140,29 +142,29 @@
   \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{
@@ -184,16 +186,6 @@ 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,