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

# S3 method for ancestral
plot(x, which = c("pie", "seqlogo"), site = 1,
  node = getRoot(x$tree), col = NULL, cex.pie = 0.5,
  pos = "bottomright", scheme = NULL, start = 1, end = 10, ...)

plotAnc(x, i = 1, col = NULL, cex.pie = 0.5, pos = "bottomright",
  scheme = NULL, ...)

plotSeqLogo(x, node = getRoot(x$tree), start = 1, end = 10,
  scheme = "Ape_NT", ...)

Arguments

x

an object of class ancestral.

which

either "pie" or "seqlogo"

node

to plot for which the probabilities should be plotted.

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.

start

start position to plot.

end

end position to plot.

...

Further arguments passed to or from other methods.

i, site

plots the i-th site.

Details

For further details see vignette("Ancestral").

See also

ancestral.pml, plot.phylo, image.DNAbin, image.AAbin ggseqlogo

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(anc.p, 3, pos="topright")

plotSeqLogo(anc.p, node="Node10", 1, 25)
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.


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

plotAnc(anc.ch, 21, scheme="Ape_AA", pos="topleft")

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

plotSeqLogo(anc.ch, node="Node1", 1, 25, scheme="Clustal")
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.