Usage
densityMap(trees, res=100, fsize=NULL, ftype=NULL, lwd=3, check=FALSE,
legend=NULL, outline=FALSE, type="phylogram", direction="rightwards",
plot=TRUE, ...)
## S3 method for class 'densityMap':
plot(x, ...)
Arguments
trees
set of phylogenetic trees in a modified "multiPhylo" object. Values for a discrete character are mapped on the tree. See make.simmap and read.simma res
resolution for gradient plotting. Larger numbers indicate a finer (smoother) gradient.
fsize
relative font size - can be a vector with the second element giving the font size for the legend.
ftype
font type - see options in plotSimmap. As with fsize, can be a vector with the second element giving font type for the legend. lwd
line width for branches.
check
check to make sure that the topology and branch lengths of all phylogenies in trees are equal.
legend
if FALSE no legend is plotted; if a numeric value, it gives the length of the legend in units of branch length. Default is 0.5 times the total tree length.
outline
logical value indicating whether or not to outline the branches of the tree in black.
type
type of plot desired. Options are "phylogram" for a rightward square phylogram; and "fan" for a circular phylogram.
plot
logical value indicating whether or not to plot the tree. If plot=FALSE then an object of class "densityMap" will be returned without plotting.
direction
plotting direction for type="phylogram".
x
for plot.densityMap, an object of class "densityMap".
...
optional arguments for plot.densityMap. These include all the arguments of densityMap except trees and res.