normalizeTaxa: Bring multiple raw taxonomies into alignment

In taxonomizr: Functions to Work with NCBI Accessions and Taxonomy

Bring multiple raw taxonomies into alignment

Description

Combine the raw taxonomy of several taxa into a single matrix where each row corresponds to a taxa and each column a taxonomic level. Named taxonomic levels are aligned between taxa then any unspecified clades are combined between the named levels. Taxonomic levels between named levels are arbitrarily combined from most generic to most specific. Working from the data provided in the NCBI taxonomy results in ambiguities so results should be used with care.

Usage

normalizeTaxa(
  rawTaxa,
  cladeRegex = "^clade$|^clade\\.[0-9]+$|^$|no rank",
  rootFill = "_ROOT_",
  lineageOrder = c()
)

Arguments

rawTaxa	A list of vectors with each vector containing a named character vector with entries specifying taxonomy for a clade and names giving the corresponding taxonomic levels e.g. the output from getRawTaxonomy
cladeRegex	A regex to identify ambiguous taxonomic levels. In the case of NCBI taxonomy, these unidentified levels are all labelled "clade" and getRawTaxonomy may attach a unique digit attach to the end for uniqueness.
rootFill	If a clade is upstream of the highest taxonomic level then it will be labeled with this prefix
lineageOrder	A vector giving an ordering for lineages from most specific to most generic. This should be unnecessary unless the taxonomy contains ambiguities e.g. one taxa goes from species to kingdom while another goes from genus to kingdom leaving it ambiguous whether genus or species is more specific

Value

a matrix with a row for each taxa and a column for each taxonomic level

See Also

getRawTaxonomy

Examples

rawTaxa<-list(
   '81907' = c(species = "Alectura lathami", genus = "Alectura",
     family = "Megapodiidae", order = "Galliformes", superorder = "Galloanserae",
     infraclass = "Neognathae", class = "Aves", clade = "Coelurosauria",
     clade.1 = "Theropoda", clade.2 = "Saurischia", clade.3 = "Dinosauria",
     clade.4 = "Archosauria", clade.5 = "Archelosauria", clade.6 = "Sauria",
     clade.7 = "Sauropsida", clade.8 = "Amniota", clade.9 = "Tetrapoda",
     clade.10 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.11 = "Euteleostomi", clade.12 = "Teleostomi", clade.13 = "Gnathostomata",
     clade.14 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.15 = "Deuterostomia", clade.16 = "Bilateria", clade.17 = "Eumetazoa",
     kingdom = "Metazoa", clade.18 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms"),
   '8496' = c(species = "Alligator mississippiensis",
     genus = "Alligator", subfamily = "Alligatorinae", family = "Alligatoridae",
     order = "Crocodylia", clade = "Archosauria", clade.1 = "Archelosauria",
     clade.2 = "Sauria", clade.3 = "Sauropsida", clade.4 = "Amniota",
     clade.5 = "Tetrapoda", clade.6 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.7 = "Euteleostomi", clade.8 = "Teleostomi", clade.9 = "Gnathostomata",
     clade.10 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.11 = "Deuterostomia", clade.12 = "Bilateria", clade.13 = "Eumetazoa",
     kingdom = "Metazoa", clade.14 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms"),
   '38654' = c(species = "Alligator sinensis",
     genus = "Alligator", subfamily = "Alligatorinae", family = "Alligatoridae",
     order = "Crocodylia", clade = "Archosauria", clade.1 = "Archelosauria",
     clade.2 = "Sauria", clade.3 = "Sauropsida", clade.4 = "Amniota",
     clade.5 = "Tetrapoda", clade.6 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.7 = "Euteleostomi", clade.8 = "Teleostomi", clade.9 = "Gnathostomata",
     clade.10 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.11 = "Deuterostomia", clade.12 = "Bilateria", clade.13 = "Eumetazoa",
     kingdom = "Metazoa", clade.14 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms")
)
normalizeTaxa(rawTaxa)

taxonomizr documentation built on May 29, 2024, 8:49 a.m.