Plot ancestral character on a tree

plotAnc plots a phylogeny and adds character to the nodes. Either takes output from ancestral.pars or ancestral.pml or from an alignment where there are node labels in the tree match the constructed sequences in the alignment.

Usage

plotAnc(tree, data, i = 1, site.pattern = FALSE, col = NULL,
  cex.pie = 0.5, pos = "bottomright", scheme = NULL, ...)

Arguments

tree

a tree, i.e. an object of class pml

data

an object of class phyDat or ancestral.

i

plots the i-th site of the data.

site.pattern

logical, plot i-th site pattern or i-th site

col

a vector containing the colors for all possible states.

cex.pie

a numeric defining the size of the pie graphs.

pos

a character string defining the position of the legend.

scheme

a predefined color scheme. For amino acid options are "Ape_AA", "Zappo_AA", "Clustal", "Polarity" and "Transmembrane_tendency", for nucleotides "Ape_NT" and"RY_NT". Names can be abbreviated.

...

Further arguments passed to or from other methods.

Details

For further details see vignette("Ancestral").

See also

ancestral.pml, plot.phylo

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

example(NJ)
#> 
#> NJ> data(Laurasiatherian)
#> 
#> NJ> dm <- dist.ml(Laurasiatherian)
#> 
#> NJ> tree <- NJ(dm)
#> 
#> NJ> plot(tree)

# generate node labels to ensure plotting will work
tree <- makeNodeLabel(tree)
anc.p <- ancestral.pars(tree, Laurasiatherian)
# plot the third character
plotAnc(tree, anc.p, 3)


data(chloroplast)
tree <- pratchet(chloroplast,  maxit=10, trace=0)
tree <- makeNodeLabel(tree)
anc.ch <- ancestral.pars(tree, chloroplast)
image(chloroplast[, 1:25])

#> NULL
plotAnc(tree, anc.ch, 21, scheme="Ape_AA")

plotAnc(tree, anc.ch, 21, scheme="Clustal")