plot.equivalent_shifts: Plot all the equivalent solutions.

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Plot all the equivalent solutions.

Description

plot.equivalent_shifts plots a representation of all the equivalent shifts allocations, with a representation of the shifts and their values, and a coloration of the branches in term of regimes.

Usage

## S3 method for class 'equivalent_shifts'
plot(
  x,
  trait = 1,
  show_shifts_values = TRUE,
  numbering = FALSE,
  colors_tips = NULL,
  nbr_col = 3,
  gray_scale = FALSE,
  edge.width = 2,
  shifts_cex = 1.2,
  ...
)

Arguments

x	an object of class equivalent_shifts, result of function equivalent_shifts
trait	(integer) the trait to be plotted, if multivariate. Default to 1.
show_shifts_values	whether to show the equivalent shifts values or not. Default to FALSE.
numbering	whether to number the solutions. Default to FALSE.
colors_tips	user-provided colors for the tips of the tree. A vector vector with as many colors as there are tips. Will be automatically computed if not provided.
nbr_col	the number of columns on which to display the plot. Default to 3.
gray_scale	if TRUE, the colors are replaced by a gray scale. Default to FALSE.
edge.width	width of the edge. Default to 1.
shifts_cex	if value_in_box=TRUE, the size of the text in the boxes. Default to 0.8.
...	further arguments to be passed to plot.phylo.

Details

This function uses function plot.phylo for the actual plotting of the trees.

Value

A plot of the equivalent shifts allocations.

See Also

equivalent_shifts, plot.phylo

PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.