R: Plot all the equivalent solutions.

plot.equivalent_shifts {PhylogeneticEM} | R Documentation

## 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`

[Package PhylogeneticEM version 1.1.0 Index]