phylosignal (version 1.3.1)

plot.phylosim: Plot phylosim object

Description

This function plots a phylosim object to visualize the behaviour of phylogenetic signal statistics for a given phylogenetic tree

Usage

# S3 method for phylosim
plot(
  x,
  what = c("stat", "pval"),
  stacked.methods = FALSE,
  quantiles = c(0.05, 0.95),
  col = 1:5,
  legend = TRUE,
  ...
)

Arguments

x

a phylosim object.

what

what to represent on the plot. Can be the statistics used to measure the signal ("stat") or the p-values ("pval").

stacked.methods

a logical. If different methods have been used, should they be plotted on the same graphic (TRUE) or not (FALSE, default).

quantiles

a vector of two numeric values between 0 and 1 giving the minimum and the maximum quantiles to plot. Set to NULL to not plot quantiles.

col

a vector of colors for the different methods.

legend

a logical. If stacked.methods is set to TRUE, should a legend be printed to differentiate the different methods?

...

further arguments to be passed to or from other methods.

See Also

phyloSim.

Examples

if (FALSE) {
data(navic)
psim <- phyloSim(navic)
plot(psim)
plot.phylosim(psim, what = "pval", stacked.methods = TRUE)
}