plotSimmap {phytools}

Plot stochastic character mapped tree

Description

Plots one or multiple stochastic character mapped trees.

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)
## S3 method for class 'simmap'
plot(x, ...)
## S3 method for class 'multiSimmap'
plot(x, ...)

Arguments

tree

an object of class "simmap" or "multiSimmap" containing a stochastic mapping or set of mappings (e.g., see read.simmap & make.simmap).

colors

a vector with names translating the mapped states to colors - see Examples.

fsize

relative font size for tip labels.

ftype

font type - options are "reg", "i" (italics), "b" (bold), or "bi" (bold-italics).

lwd

line width for plotting.

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 FALSE.

node.numbers

a logical value indicating whether or not node numbers should be plotted.

mar

vector containing the margins for the plot to be passed to par. If not specified, the default margins are [0.1,0.1,0.1,0.1].

add

a logical value indicating whether or not to add the plotted tree to the current plot (TRUE) or create a new plot (FALSE, the default).

offset

offset for the tip labels in character widths.

direction

plotting direction. Options are "rightwards" (the default), "leftwards", "upwards" or "downwards". For method="fan" direction is ignored.

type

plot type. Can be "phylogram", "fan", or "cladogram". Only a subset of options are presently available for type="fan".

setEnv

logical value indicating whether or not to set the environment .PlotPhyloEnv. Setting this to TRUE (the default) will allow compatibility with ape labeling functions such as nodelabels.

part

value between 0 and 1 for type="fan" indicating what fraction of the full circular tree to use as plotting area. For instance, part=0.5 will plot a half fan phylogeny. It also affects the axis scaling used.

xlim

x-limits for the plot.

ylim

y-limits for the plot.

nodes

node placement following Felsenstein (2004; pp. 574-576). Can be "intermediate", "centered", "weighted", or "inner". So far only works for type="phylogram".

tips

labeled vector containing the vertical position of tips. Normally this will be 1:N for N tips in the tree.

maxY

maximum value of y to use before rotating a tree into fan configuration. This will only make a difference if different from Ntip(tree).

hold

logical argument indicating whether or not to hold the output to the graphical device before plotting. Defaults to hold=TRUE.

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.

lend

line end style. See par.

asp

aspect ratio. See plot.window.

outline

logical value indicating whether or not to draw a black outline around the plotted edges of the tree.

plot

logical value indicating whether or not to actually plot the tree. (See equivalent argument in plot.phylo.)

underscore

logical value indicating whether to plot the underscore character, "_" (if underscore=TRUE) or substitute for a space. Defaults to underscore=FALSE.

arc_height

for type="arc" trees, the height of the arc in units of total tree depth.

x

for S3 plotting method, object of class "simmap" or "multiSimmap".

...

for S3 plotting method, other arguments to be passed to plotSimmap.

Value

Plots a tree.

Author(s)

Liam Revell [e-mail]

References

Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.

Felsenstein, J. (2004) Inferring Phylogenies. Sinauer.

Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138.

Revell, L. J. (2014) Graphical methods for visualizing comparative data on phylogenies. Chapter 4 in 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). PeerJ, 12, e16505.

See Also

densityMap, make.simmap, read.simmap

Examples

data(anoletree)
cols<-setNames(c("green","#E4D96F","darkgreen",
    "brown","black","darkgrey"),
    c("CG","GB","TC","TG","Tr","Tw"))
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)
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margins to default