plottree {markophylo} | R Documentation |
Plot the tree used with different hypothesized branch groupings (or clades) following unique rates coloured differently.
Description
Plotting command for use on an object of class "markophylo".
Usage
plottree(x, colors = NULL, ...)
Arguments
x |
An object of class "markophylo". |
colors |
Default works well. However, a custom vector of colours can be specified here—should be the same length as length(x$bg). Note that these colours are used to colour the different branch groupings following their own rates. |
... |
Any further commands to ape::plot.phylo. |
Value
Plotting function. See examples
Author(s)
Utkarsh J. Dang and G. Brian Golding
See Also
See also estimaterates
.
Examples
data(simdata2)
model2 <- estimaterates(usertree = simdata2$tree, userphyl = simdata2$data,
alphabet = c(1, 2), bgtype = "ancestornodes", bg = c(7),
rootprob = "equal", modelmat = matrix(c(NA, 1, 2, NA), 2, 2))
plottree(model2, colors=c("blue", "darkgreen"), edge.width = 2, show.tip.label = FALSE,
no.margin = TRUE)
ape::nodelabels(frame = "circle", cex = 0.7)
ape::tiplabels(frame = "circle", cex = 0.7)
[Package markophylo version 1.0.9 Index]