Usage
phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outfile=NULL,...)
Arguments
sp.plot
a community dataset in spacodiR format (see as.spacodi
) phy
a phylogenetic tree of class phylo
; see read.tree
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 par
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