View source: R/plot_Contsimmap.R
plot.contsimmap | R Documentation |
This function runs the default plotting method for continuous stochastic character maps (class "contsimmap
").
## S3 method for class 'contsimmap'
plot(
contsimmap,
traits = 1,
sims = sample(dim(contsimmap)[3], min(20, dim(contsimmap)[3])),
edges = NULL,
Col.by = c("simulation", "state", "edge", "time", dimnames(contsimmap)[[2]]),
Layer.by = NULL,
Alpha.by = NULL,
Mix.by = NULL,
Wgt.by = NULL,
Lty.by = NULL,
Lwd.by = NULL,
add = FALSE,
reverse.layers = FALSE,
polarize = FALSE,
ang.min = 0,
ang.max = 2 * pi,
curviness = 1,
...
)
contsimmap |
An object of class " |
traits |
A character/numeric vector specifying which traits within Alternatively, phylogenies may be plotted in more traditional styles akin to
the |
sims |
A character/numeric vector specifying which simulations within |
edges |
A character/numeric vector specifying which edges within |
Col.by , Layer.by , Alpha.by , Mix.by , Wgt.by , Lty.by , Lwd.by |
Any unambiguous abbreviation of "simulation", "state", "edge", "time", or trait
names within |
add |
|
reverse.layers |
|
polarize |
|
ang.min |
If |
ang.max |
If |
curviness |
If |
... |
Just about any base R graphical argument you can think of–it should theoretically all work! Notably, entries of
There are also a few additional and potentially important arguments:
|
Invisibly assigns plot information to "last_plot.phylo
" in
.PlotPhyloEnv
environment, just like the plot.phylo()
function from ape. Most importantly, this allows the use of the
ape functions nodelabels()
, tiplabels()
, and
edgelabels()
for further plot annotation. Note that tip/node
coordinates are averaged if multiple simulations are plotted at once.
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