Creates a distance object based on taxonomy information.

Creates a distance matrix based on taxonomy information

Usage

taxonomy_distance(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 dist object containing taxonomic distances between OTUs.

Details

In some data analyses involving OTU data, it is often useful to quantify the relatedness of OTUs based on their taxonomy. This function creates a distance matrix from a taxonomy table of the same format as output by vs_sintax. This means taxonomy_table must have columns domain, phylum, class, order, family, genus and species. It must also have a column Header with a text that unique to each row. These are used as row/column names in the returned dist object.

Distances between two OTUs reflect how high up in the taxonomy they have a common taxon, i.e if they are distinct OTUs but of the same species the distance is 1, if they are different species but same genus the distance is 2 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 3 (implicitly assuming they are different genera but same family).

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).

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)

# Calculate distance matrix
tax.dist <- taxonomy_distance(tax.tbl)

# You can now directly use 'tax.dist' with functions like hclust or ape::nj
tax.tree <- ape::nj(tax.dist)
} # }