fix in drop.tip() and new option in pic()

[ape.git] / man / nodelabels.Rd

diff --git a/man/nodelabels.Rd b/man/nodelabels.Rd
index be732b66f55540b644f3cac7ee60c851b2b42ea0..5c44f3f74d54941c5d8100ce626807a9f198281b 100644 (file)
--- a/man/nodelabels.Rd
+++ b/man/nodelabels.Rd
@@ -11,13 +11,16 @@
 \usage{
 nodelabels(text, node, adj = c(0.5, 0.5), frame = "rect",
            pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
-           col = "black", bg = "lightblue", ...)
+           col = "black", bg = "lightblue", horiz = FALSE,
+           width = NULL, height = NULL, ...)
 tiplabels(text, tip, adj = c(0.5, 0.5), frame = "rect",
           pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
-          col = "black", bg = "yellow", ...)
+          col = "black", bg = "yellow", horiz = FALSE,
+          width = NULL, height = NULL, ...)
 edgelabels(text, edge, adj = c(0.5, 0.5), frame = "rect",
            pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
-           col = "black", bg = "lightgreen", ...)
+           col = "black", bg = "lightgreen", horiz = FALSE,
+           width = NULL, height = NULL, date = NULL, ...)
 
 }
 \arguments{
@@ -30,9 +33,10 @@ edgelabels(text, edge, adj = c(0.5, 0.5), frame = "rect",
   \item{edge}{a vector of mode numeric giving the numbers of the edges
     where the text or the symbols are to be printed. Can be left empty.}
   \item{adj}{one or two numeric values specifying the horizontal and
-    vertical, respectively, justification of the text. By default, the
-    text is centered horizontally and vertically. If a single value is
-    given, this alters only the horizontal position of the text.}
+    vertical, respectively, justification of the text or symbols. By
+    default, the text is centered horizontally and vertically. If a
+    single value is given, this alters only the horizontal position of
+    the text.}
   \item{frame}{a character string specifying the kind of frame to be
     printed around the text. This must be one of "rect" (the default),
     "circle", "none", or any unambiguous abbreviation of these.}
@@ -56,6 +60,11 @@ edgelabels(text, edge, adj = c(0.5, 0.5), frame = "rect",
     \code{points} functions (e.g. \code{cex} to alter the size of the
     text or the symbols, or \code{font} for the text; see the examples
     below).}
+  \item{horiz, width, height}{parameters controlling the aspect of
+    thermometers; by default, their width and height are determined
+    automatically.}
+  \item{date}{specifies the positions of labels on edges of chronograms
+    with respect to the time scale.}
 }
 \details{
   These three functions have the same optional arguments and the same
@@ -79,10 +88,10 @@ edgelabels(text, edge, adj = c(0.5, 0.5), frame = "rect",
   \code{show.tip.label}) of \code{plot.phylo} in most cases (see the
   examples).
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}, Ben Bolker
-  \email{bolker@zoo.ufl.edu}, and Jim Lemon}
+\author{Emmanuel Paradis, Ben Bolker, and Jim Lemon}
 \seealso{
-  \code{\link{plot.phylo}}
+  \code{\link{plot.phylo}}, \code{\link{edges}},
+  \code{\link{mixedFontLabel}}
 }
 \examples{
 tr <- read.tree(text = "((Homo,Pan),Gorilla);")
@@ -139,6 +148,10 @@ text(4.5, 15, "Are you \"pie\"...", font = 4, cex = 1.5)
 plot(tr, "c", FALSE, no.margin = TRUE)
 nodelabels(thermo = x, col = rainbow(4), cex = 1.3)
 text(4.5, 15, "... or \"thermo\"?", font = 4, cex = 1.5)
+plot(tr, "c", FALSE, no.margin = TRUE)
+nodelabels(thermo = x, col = rainbow(4), cex = 1.3)
+plot(tr, "c", FALSE, no.margin = TRUE)
+nodelabels(thermo = x, col = rainbow(4), width = 3, horiz = TRUE)
 layout(matrix(1))
 plot(tr, main = "Showing Edge Lengths")
 edgelabels(round(tr$edge.length, 3), srt = 90)