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