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

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

add_mutations(x, pos = NULL, frame = "none", ...)

Arguments

x

an object of class ancestral.

i

plots the i-th site.

type

a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial", "tidy", or any unambiguous abbreviation of these.

...

Further arguments passed to or from other methods.

col

a vector containing the colors for all possible states.

cex.pie

a numeric defining the size of the pie graphs.

pos

position or range in the alignment to add mutations. If NULL all mutations are written out.

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.

node

to plot for which the probabilities should be plotted.

start

start position to plot.

end

end position to plot.

frame

a character string specifying the kind of frame to be printed around the text. See edgelabels.

Value

plotAnc returns silently x.

plotSeqLogo returns a ggplot object.

add_mutations adds the position and and changes of possible mutations to a phylogeny.

Details

For further details see vignette("Ancestral").

See also

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

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 <- anc_pars(tree, Laurasiatherian)
# plot the third character
plotAnc(anc.p, 3, pos="topright")

plotSeqLogo(anc.p, node="Node10", 1, 25)


data(chloroplast)
tree <- pratchet(chloroplast,  maxit=10, trace=0)
tree <- makeNodeLabel(tree)
anc.ch <- anc_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")



data(woodmouse)
tree <- pml_bb(woodmouse, "JC", rearrangement="NNI")$tree |> midpoint()
#> optimize edge weights:  -1858.403 --> -1857.165 
#> optimize edge weights:  -1857.165 --> -1857.165 
#> optimize topology:  -1857.165 --> -1856.056  NNI moves:  2 
#> optimize edge weights:  -1856.056 --> -1856.056 
#> optimize topology:  -1856.056 --> -1856.056  NNI moves:  0 
woodmouse_aa <- trans(woodmouse, 2) |> as.phyDat()
#> Warning: sequence length not a multiple of 3: 2 nucleotides dropped
anc_aa <- anc_pars(tree, woodmouse_aa)
plot(tree)
add_mutations(anc_aa, adj = c(.5, -0.3), col=2)