View source: R/ancestral_generics.R
write.ancestral | R Documentation |
write.ancestral
allows to export ancestral reconstructions. It writes
out the tree, a tab delimited text file with the probabilities and the
alignment. ancestral
generates an object of class ancestral.
write.ancestral(x, file = "ancestral")
as.ancestral(tree, prob, align = NULL)
## S3 method for class 'ancestral'
print(x, ...)
## S3 method for class 'ancestral'
as.phyDat(x, ...)
## S3 method for class 'ancestral'
as.data.frame(x, ...)
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. |
This allows also to read in reconstruction made by iqtree to use the plotting capabilities of R.
write.ancestral
returns the input x invisibly.
anc_pml
, plotAnc
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_align.fasta", format="fasta")
tree <- read.tree("ancestral_tree.nwk")
df <- read.table("ancestral.state", header=TRUE)
anc_ml_disc <- as.ancestral(tree, df, align)
plotAnc(anc_ml_disc, 20)
unlink(c("ancestral_align.fasta", "ancestral_tree.nwk", "ancestral.state"))
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