plottree: Plot the tree used the branches colored according to the different specified branch groupings (or clades) following unique rates.

Description

Plotting command for use on an object of class "indelmiss".

Usage

plottree(x, toilabel = TRUE, colors = NULL, ...)

Value

Plot the tree used the branches colored according to the different specified branch groupings (or clades) following unique rates.

Arguments

x: An object of class "indelmiss".
toilabel: If this is TRUE, a plus sign is printed next to the taxa of interest for which a missing data proportion was estimated. Note that the taxa labels being referred to can be seen by using ape::tiplabels().
colors: Vector of colours the same length as length(x$bg). Note that these colours are used to colour the different branch groupings associated with unique insertion and/or deletion rates.
...: Any further commands to ape::plot.phylo.

Author

Utkarsh J. Dang and G. Brian Golding

utkarshdang@cunet.carleton.ca

Examples

Run this code

indel <- indelrates(datasource = "simulation", seed = 1, taxa = 5,
             mu = 1, nu = 5, phyl = 5000,  pmiss = 0, toi = 1, 
             bgtype="ancestornodes", bg = 7, 
             zerocorrection = TRUE, 
             modelnames = c("M1", "M2", "M3", "M4"),
             optmethod = "nlminb")
print(indel)
plottree(indel,colors=c("blue","red"))
ape::tiplabels()