plottree {indelmiss}

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, ...)

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.

Value

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

Author(s)

Utkarsh J. Dang and G. Brian Golding

[e-mail]

See Also

See also plot.indelmiss and plot.phylo.

Examples

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()