Make a taxonomy tree — taxonomy

Creates a phylo object based on taxonomy

Usage

taxonomy_tree(taxonomy_table, confidence = NULL)

Arguments

taxonomy_table: (Required). A data.frame with taxonomy information, see Details.
confidence: (Optional). A threshold value used to replace taxa with confidence scores below this to NA.

Value

A phylo object, see nj.

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.

The distances between OTUs are computed by taxonomy_distance.

From these distances a Neighbor Joining tree is built using nj.

References

https://www.biorxiv.org/content/10.1101/074161v1

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)
} # }