Export and convenience functions for ancestral reconstructions

write.ancestral allows to export ancestral reconstructions. It writes out the tree, a tab delimited text file with the probabilities, an alignment of the the extant sequences and the most likely ancestral states. And a unaligned fasta file containg the most likely ancestral states. ancestral generates an object of class ancestral.

Usage

write.ancestral(x, file = "ancestral")

as.ancestral(tree, prob, align, ...)

# S3 method for class 'ancestral'
print(x, ...)

# S3 method for class 'ancestral'
as.phyDat(x, ...)

# S3 method for class 'ancestral'
as.data.frame(x, ..., terminal = FALSE)

Arguments

x: an object of class ancestral
file: a file name. File endings are added.
tree: an object of class phylo.
prob: an data.frame containing a matrix of posterior probabilities for each state and site.
align: an object of class phyDat.
...: Further arguments passed to or from other methods.
terminal: logical, should terminal nodes included.

Value

write.ancestral returns the input x invisibly.

Details

This allows also to read in reconstruction made by iqtree to use the plotting capabilities of R.

Examples

data(Laurasiatherian)
fit <- pml_bb(Laurasiatherian[,1:100], "JC", rearrangement = "none")
anc_ml <- anc_pml(fit)
write.ancestral(anc_ml)
# Can be also results from iqtree
align <- read.phyDat("ancestral_all.fasta", format="fasta")
tree <- read.tree("ancestral_tree.nwk")
df <- read.table("ancestral_state.tsv.gz", header=TRUE)
anc_ml_disc <- as.ancestral(tree, df, align)

plotAnc(anc_ml_disc, 20)


heatmapp(tree, align, nodes=TRUE)


unlink(c("ancestral_all.fasta", "ancestral_tree.nwk",
         "ancestral_state.tsv.gz", "ancestral_state.fasta"))