Plot phylosim object

Share:

Description

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

Usage

1
2
3
4
## S3 method for class '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

1
2
3
4
5
6
7
## Not run: 
data(navic)
psim <- phyloSim(navic)
plot(psim)
plot.phylosim(psim, what = "pval", stacked.methods = TRUE)

## End(Not run)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.