Creates a phylo object based on taxonomy
Details
In some data analyses involving OTU data a phylogenetic tree describing the relatedness of the OTUs is required. To construct such trees you typically need to make a multiple alignment of the sequences behind each OTU, which is a huge job.
An alternative is then to simply use the taxonomy, and create a
'taxonomy-tree' instead of a phylogenetic tree. This function creates such a
tree from a taxonomy table of the same format as output by
vs_sintax.
Distances between two OTUs reflect how high up in the taxonomy they have a
common taxon, i.e if they are of the same species the distance is 0, if
different species but same genus the distance is 1 etc. Note that NAs
in the taxonomy are not matched, increasing the distances, i.e if two OTUs
have NA as species and genus, but share family, the distance is 2.
The confidence sets a threshold for replacing low-confidence taxa to
NA. For this to work the taxonomy_table must have columns with
such confidence scores i.e. columns domain_score, phylum_score,
...species_score. If the species_score is below confidence the
corresponding species name is set to NA, and similar for all ranks.
The default is to ignore this confidence (confidence = NULL).
From these distances a Neighbor Joining tree is built using nj.
Examples
if (FALSE) { # \dontrun{
# Assign taxonomy with sintax
db.file <- file.path(file.path(path.package("Rsearch"), "extdata"),
"sintax_db.fasta")
fasta.file <- file.path(file.path(path.package("Rsearch"), "extdata"),
"small.fasta")
tax.tbl <- vs_sintax(fasta_input = fasta.file, database = db.file)
# Making tree
tax.tree <- taxonomy_tree(tax.tbl)
} # }