[Adephylo-commits] r192 - in pkg: R man

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2013-05-16 15:48:51 +0200 (Thu, 16 May 2013)
New Revision: 192

Added:
   pkg/man/bullseye.Rd
Modified:
   pkg/R/bullseye.R
Log:
resolving conflict (?)

Modified: pkg/R/bullseye.R
===================================================================
--- pkg/R/bullseye.R	2013-05-15 16:43:12 UTC (rev 191)
+++ pkg/R/bullseye.R	2013-05-16 13:48:51 UTC (rev 192)
@@ -36,11 +36,6 @@
         col.tips.by <- unlist(col.tips.by)
         names(col.tips.by) <- old.names
     }
-    if(!is.null(col.tips.by) && is.matrix(col.tips.by)){
-        old.names <- rownames(col.tips.by)
-        col.tips.by <- as.vector(col.tips.by)
-        names(col.tips.by) <- old.names
-    }
     if(!is.null(col.tips.by) && !is.null(names(col.tips.by))){
         col.tips.by <- col.tips.by[phy$tip.label]
     }

Added: pkg/man/bullseye.Rd
===================================================================
--- pkg/man/bullseye.Rd	                        (rev 0)
+++ pkg/man/bullseye.Rd	2013-05-16 13:48:51 UTC (rev 192)
@@ -0,0 +1,74 @@
+\name{bullseye}
+\alias{bullseye}
+\title{Fan-like phylogeny with possible representation of traits on tips}
+\description{
+  This function represents a phylogeny as a fan, using circles to
+  provide a legend for distances and optionally colored symbols to
+  represent traits associated to the tips of the tree. This function
+  uses and is compatible with ape's \code{\link[ape]{plot.phylo}}.
+}
+\usage{
+bullseye(phy, traits=NULL, col.tips.by=NULL, col.pal=seasun,
+         circ.n=6, circ.bg=transp("royalblue",.1), circ.unit=NULL,
+         legend=TRUE, leg.posi="bottomleft", leg.title="", leg.bg="white",
+         traits.inset=1.1, traits.space=0.05, traits.pch=19, traits.cex=1,
+         alpha=1, axis=TRUE,\dots)
+}
+\arguments{
+  \item{phy}{a tree in \code{phylo}, \linkS4class{phylo4} or
+    \linkS4class{phylo4d} format.}
+  \item{traits}{an optional data.frame of traits.}
+  \item{col.tips.by}{an optional vector used to define colors for tip
+    labels; if unamed, must be ordered in the same order as
+    \code{phy$tip.label}.}
+  \item{col.pal}{a function generating colors according to a given
+    palette; several palettes can be provided as a list, in the case of
+    several traits; the first palette is always reserved for the tip
+    colors; this argument is recycled.}
+  \item{circ.n}{the number of circles for the distance annotations.}
+  \item{circ.bg}{the color of the circles.}
+  \item{circ.unit}{the unit of the circles; if NULL, determined
+    automatically from the data.}
+  \item{legend}{a logical specifying whether a legend should be
+    plotted; only one legend is displayed, with priority to tip colors
+    first, and then to the first trait.}
+  \item{leg.posi,leg.title,leg.bg}{position, title and background for the legend.}
+  \item{traits.inset}{inset for positioning the traits; 1 corresponds to
+    the circle crossing the furthest tip, 0 to the center of the plot.}
+  \item{traits.space}{a coefficient indicating the spacing between traits.}
+  \item{traits.pch,traits.cex}{type and size of the symbols used for the
+    traits; recycled if needed.}
+  \item{alpha}{alpha value to be used for the color transparency,
+    between 0 (invisible) and 1 (plain).}
+  \item{axis}{a logical indicating whether an axis should be displayed.}
+  \item{\dots}{further arguments to be passed to plot methods from
+    \code{ape}. See \code{\link[ape]{plot.phylo}}.}
+}
+\seealso{
+  \code{\link{table.phylo4d}} for non-radial plots.\cr
+
+  The \linkS4class{phylo4d} class for storing \code{phylogeny+data}.\cr
+
+  \code{\link[ape]{plot.phylo}} from the \code{ape} package.\cr
+
+  \code{\link[ade4]{dotchart.phylog}}.
+}
+\author{Thibaut Jombart \email{tjombart at imperial.ac.uk}}
+\examples{
+
+data(lizards)
+tre <- read.tree(text=lizards$hprA) # make a tree
+
+## basic plots
+bullseye(tre)
+bullseye(tre, lizards$traits)
+
+## customized
+par(mar=c(6,6,6,6))
+bullseye(tre, lizards$traits, traits.cex=sqrt(1:7), alpha=.7,
+         legend=FALSE, circ.unit=10, circ.bg=transp("black",.1),
+         edge.width=2)
+
+}
+\keyword{hplot}
+\keyword{multivariate}