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

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Description

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

Usage

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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.

Author(s)

Utkarsh J. Dang and G. Brian Golding

udang@mcmaster.ca

See Also

See also plot.indelmiss and plot.phylo.

Examples

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#indel <- indelrates(datasource = "simulation", seed = 1, taxa = 5,
#             mu = 1, nu = 5, phyl = 5000,  nmiss = 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()