plot.ancestral: Plot ancestral character on a tree

In phangorn: Phylogenetic Reconstruction and Analysis

Plot ancestral character on a tree

Description

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, 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	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.
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.

Details

For further details see vignette("Ancestral").

Value

plotAnc returns silently x.

plotSeqLogo returns a ggplot object.

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

Author(s)

Klaus Schliep [e-mail]

See Also

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

Examples

example(NJ)
# 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()
woodmouse_aa <- trans(woodmouse, 2) |> as.phyDat()
anc_aa <- anc_pars(tree, woodmouse_aa)
plot(tree, direction="downwards")
add_mutations(anc_aa)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.