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\name{plotSimmap}
\alias{plotSimmap}
\alias{plot.simmap}
\alias{plot.multiSimmap}
\title{Plot stochastic character mapped tree}
\usage{
plotSimmap(tree, colors=NULL, fsize=1.0, ftype="reg", lwd=2, pts=FALSE,
node.numbers=FALSE, mar=NULL, add=FALSE, offset=NULL,
direction="rightwards", type="phylogram", setEnv=TRUE,
part=if(type=="arc") 0.5 else 1.0, xlim=NULL, ylim=NULL,
nodes="intermediate", tips=NULL, maxY=NULL, hold=TRUE,
split.vertical=FALSE, lend=2, asp=NA, outline=FALSE,
plot=TRUE, underscore=FALSE, arc_height=2)
\method{plot}{simmap}(x, ...)
\method{plot}{multiSimmap}(x, ...)
}
\arguments{
\item{tree}{an object of class \code{"simmap"} or \code{"multiSimmap"} containing a stochastic mapping or set of mappings (e.g., see \code{\link{read.simmap}} & \code{\link{make.simmap}}).}
\item{colors}{a vector with names translating the mapped states to colors - see \code{Examples}.}
\item{fsize}{relative font size for tip labels.}
\item{ftype}{font type - options are \code{"reg"}, \code{"i"} (italics), \code{"b"} (bold), or \code{"bi"} (bold-italics).}
\item{lwd}{line width for plotting.}
\item{pts}{logical value indicating whether or not to plot filled circles at each vertex of the tree, as well as at transition points between mapped states. Default is \code{FALSE}.}
\item{node.numbers}{a logical value indicating whether or not node numbers should be plotted.}
\item{mar}{vector containing the margins for the plot to be passed to \code{\link{par}}. If not specified, the default margins are [0.1,0.1,0.1,0.1].}
\item{add}{a logical value indicating whether or not to add the plotted tree to the current plot (\code{TRUE}) or create a new plot (\code{FALSE}, the default).}
\item{offset}{offset for the tip labels in character widths.}
\item{direction}{plotting direction. Options are \code{"rightwards"} (the default), \code{"leftwards"}, \code{"upwards"} or \code{"downwards"}. For \code{method="fan"} \code{direction} is ignored.}
\item{type}{plot type. Can be \code{"phylogram"}, \code{"fan"}, or \code{"cladogram"}. Only a subset of options are presently available for \code{type="fan"}.}
\item{setEnv}{logical value indicating whether or not to set the environment \code{.PlotPhyloEnv}. Setting this to \code{TRUE} (the default) will allow compatibility with \pkg{ape} labeling functions such as \code{\link[ape]{nodelabels}}.}
\item{part}{value between 0 and 1 for \code{type="fan"} indicating what fraction of the full circular tree to use as plotting area. For instance, \code{part=0.5} will plot a half fan phylogeny. It also affects the axis scaling used.}
\item{xlim}{x-limits for the plot.}
\item{ylim}{y-limits for the plot.}
\item{nodes}{node placement following Felsenstein (2004; pp. 574-576). Can be \code{"intermediate"}, \code{"centered"}, \code{"weighted"}, or \code{"inner"}. So far only works for \code{type="phylogram"}.}
\item{tips}{labeled vector containing the vertical position of tips. Normally this will be \code{1:N} for \code{N} tips in the tree.}
\item{maxY}{maximum value of y to use before rotating a tree into fan configuration. This will only make a difference if different from \code{Ntip(tree)}.}
\item{hold}{logical argument indicating whether or not to hold the output to the graphical device before plotting. Defaults to \code{hold=TRUE}.}
\item{split.vertical}{split the color of the vertically plotted edges by the state of the daughter edges. Only applies if the edge state changes exactly at a node.}
\item{lend}{line end style. See \code{\link{par}}.}
\item{asp}{aspect ratio. See \code{\link{plot.window}}.}
\item{outline}{logical value indicating whether or not to draw a black outline around the plotted edges of the tree.}
\item{plot}{logical value indicating whether or not to actually plot the tree. (See equivalent argument in \code{\link[ape]{plot.phylo}}.)}
\item{underscore}{logical value indicating whether to plot the underscore character, \code{"_"}, or substitute for a space. Defaults to \code{underscore=FALSE}.}
\item{arc_height}{for \code{type="arc"} trees, the height of the arc in units of total tree depth.}
\item{x}{for S3 plotting method, object of class \code{"simmap"} or \code{"multiSimmap"}.}
\item{...}{for S3 plotting method, other arguments to be passed to \code{\link{plotSimmap}}.}
}
\description{
Plots one or multiple stochastic character mapped trees.
}
\value{
Plots a tree.
}
\references{
Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. \emph{BMC Bioinformatics}, \bold{7}, 88.
Felsenstein, J. (2004) \emph{Inferring Phylogenies}. Sinauer.
Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback (2003) Stochastic mapping of morphological characters. \emph{Systematic Biology}, \bold{52}, 131-138.
Revell, L. J. (2014) Graphical methods for visualizing comparative data on phylogenies. Chapter 4 in \emph{Modern phylogenetic comparative methods and their application in evolutionary biology: Concepts and practice} (L. Z. Garamszegi ed.), pp. 77-103.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). \emph{PeerJ}, \bold{12}, e16505.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
\code{\link{densityMap}}, \code{\link{make.simmap}}, \code{\link{read.simmap}}
}
\examples{
## load tree with mapped character
data(anoletree)
## set colors for regims
cols<-setNames(c("green","#E4D96F","darkgreen",
"brown","black","darkgrey"),
c("CG","GB","TC","TG","Tr","Tw"))
## create plot
plot(anoletree,cols,fsize=0.5,ftype="i",outline=TRUE,
lwd=3,ylim=c(0,Ntip(anoletree)),
mar=c(0.1,0.1,1.1,0.1))
add.simmap.legend(colors=cols,prompt=FALSE,x=0,y=-0.5,
vertical=FALSE)
title(main="Caribbean ecomorphs of anoles",font.main=3,
line=0)
## reset margins to default
par(mar=c(5.1,4.1,4.1,2.1))
}
\keyword{ancestral states}
\keyword{phylogenetics}
\keyword{plotting}
\keyword{comparative method}
\keyword{discrete character}
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