Description Usage Arguments Details Value Author(s) Examples
phy.dotplot
is used to visually display species membership in communities, generating one plot per community
1 |
sp.plot |
a community dataset in spacodiR format (see |
phy |
a phylogenetic tree of class |
edge.width |
a value specifying the thickness of branches on the plotted phylogen(ies) |
lab.adj |
a vector of two values, adjusting plotted group names, with respect to the x- and y-axes |
tips.adj |
a vector of two values, adjusting the position of plotted symbols (referencing the x- and y-axes) |
tips.cex |
a value for character expansion of plotted symbols for present species |
pch |
a value for the plotting character for species-presence symbols: see |
print.labs |
Boolean; returns array of tip labels, group membership of species, and tree to the console |
outfile |
an optional .pdf file to which to write output |
... |
additional plotting options to be specified |
For several groups (fewer than sixteen, for optimal visibility), this function will generate a plot of phylogenies, group labels for each
tree, and symbols demarcating a particular species that is present within the group. This may be useful in visual representations of phylogenetic overdispersion
or underdispersion within plots (or other groups). Particularly the tips.adj
option may require fiddling in order for symbols to appear precisely where they should.
A collection of trees (or a single tree), where species present within a predefined group are represented with a dark circle at the tip (if pch=21
).
Jonathan Eastman
1 2 3 4 | data(sp.example)
attach(sp.example)
phy.dotplot(sp.plot=spl[,1:9], phy=phy, tips.adj=c(0.50,0.55), lab.adj=c(0,1))
|
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