The taxonomy() function (formerly) implemented in
myTAI relies on the powerful package taxize. More specifically,
the taxonomic information retrieval has been customized for the
myTAI standard and for organism specific information
retrieval.
While the previous taxonomy() function has been
deprecated since taxize was pulled from
CRAN, users can nevertheless follow the taxonomy pipeline by installing
the taxize package and copy the old
taxonomy function.
# install taxize from CRAN
install.packages("taxize")
# if taxize is not available again
install.packages("remotes")
remotes::install_github("ropensci/taxize")Copy the taxonomy function:
open for the taxonomy function
Click on the copy icon to copy the function.
#' @title Retrieving Taxonomic Information of a Query Organism
#' @description This function takes the scientific name of a query organism
#' and returns selected output formats of taxonomic information for the corresponding organism.
#' @param organism a character string specifying the scientific name of a query organism.
#' @param db a character string specifying the database to query, e.g. \code{db} = \code{"itis"} or \code{"ncbi"}.
#' @param output a character string specifying the taxonomic information that shall be returned.
#' Implemented are: \code{output} = \code{"classification"}, \code{"taxid"}, or \code{"children"}.
#' @details This function is based on the powerful package \pkg{taxize} and implements
#' the customized retrieval of taxonomic information for a query organism.
#'
#' The following data bases can be selected to retrieve taxonomic information:
#'
#' \itemize{
#' \item \code{db = "itis"} : Integrated Taxonomic Information Service
#' \item \code{db = "ncbi"} : National Center for Biotechnology Information
#' }
#'
#'
#'
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' # retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
#' # from NCBI Taxonomy
#' taxonomy("Arabidopsis thaliana",db = "ncbi")
#'
#' # the same can be applied to database : "itis"
#' taxonomy("Arabidopsis thaliana",db = "itis")
#'
#' # retrieving the taxonomic hierarchy of "Arabidopsis"
#' taxonomy("Arabidopsis",db = "ncbi") # analogous : db = "ncbi" or "itis"
#'
#' # or just "Arabidopsis"
#' taxonomy("Arabidopsis",db = "ncbi")
#'
#' # retrieving the taxonomy id of the query organism and in the correspondning database
#' # taxonomy("Arabidopsis thaliana",db = "ncbi", output = "taxid")
#'
#' # the same can be applied to databases : "ncbi" and "itis"
#' taxonomy("Arabidopsis thaliana",db = "ncbi", output = "taxid")
#' taxonomy("Arabidopsis thaliana",db = "itis", output = "taxid")
#'
#'
#' # retrieve children taxa of the query organism stored in the correspondning database
#' taxonomy("Arabidopsis",db = "ncbi", output = "children")
#'
#' # the same can be applied to databases : "ncbi" and "itis"
#' taxonomy("Arabidopsis thaliana",db = "ncbi", output = "children")
#' taxonomy("Arabidopsis thaliana",db = "itis", output = "children")
#'
#' }
#' @references
#'
#' Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search and retrieval in R. F1000Research,
#' 2:191. URL: http://f1000research.com/articles/2-191/v2.
#'
#' Scott Chamberlain, Eduard Szocs, Carl Boettiger, Karthik Ram, Ignasi Bartomeus, and John Baumgartner
#' (2014) taxize: Taxonomic information from around the web. R package version 0.3.0.
#' https://github.com/ropensci/taxize
#' @export
taxonomy <- function(organism, db = "ncbi", output = "classification"){
if (!is.element(output,c("classification","taxid","children")))
stop ("The output '",output,"' is not supported by this function.")
if (!is.element(db,c("ncbi","itis")))
stop ("Database '",db,"' is not supported by this function.")
name <- id <- NULL
if (db == "ncbi")
tax_hierarchy <- as.data.frame(taxize::classification(taxize::get_uid(organism), db = "ncbi")[[1]])
else if (db == "itis")
tax_hierarchy <- as.data.frame(taxize::classification(taxize::get_tsn(organism), db = "itis")[[1]])
# tryCatch({colnames(tax_hierarchy) <- c("name","rank","id")},stop("The connection to ",db," did not work properly. Please check your internet connection or maybe the API did change.", call. = FALSE))
if(output == "classification"){
return(tax_hierarchy)
}
if(output == "taxid"){
return(dplyr::select(dplyr::filter(tax_hierarchy, name == organism),id))
}
if(output == "children"){
return(as.data.frame(taxize::children(organism, db = db)[[1]]))
}
}The taxonomy() function can be used to classify genomes
according to phylogenetic classification into Phylostrata
(Phylostratigraphy) or to retrieve species specific taxonomic
information when performing Divergence Stratigraphy (see Introduction for details).
For larger taxonomy queries it may be useful to create an NCBI Account and set up an ENTREZ API KEY.
# install.packages(c("taxize", "usethis"))
taxize::use_entrez()
# Create your key from your (brand-new) account's.
# After generating your key set it as ENTREZ_KEY in .Renviron.
# ENTREZ_KEY='youractualkeynotthisstring'
# For that, use usethis::edit_r_environ()
usethis::edit_r_environ()Taxonomic Information Retrieval
The taxonomy() function to retrieve taxonomic
information.
retrieve taxonomy hierarchy
In the following example we will obtain the taxonomic hierarchy of
Arabidopsis thaliana from NCBI Taxonomy.
# retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
# from NCBI Taxonomy
taxonomy( organism = "Arabidopsis thaliana",
db = "ncbi",
output = "classification" )Show output
## ══ 1 queries ═══════════════## ✔ Found: Arabidopsis+thaliana
## ══ Results ═════════════════
##
## • Total: 1
## • Found: 1
## • Not Found: 0## name rank id
## 1 cellular organisms cellular root 131567
## 2 Eukaryota domain 2759
## 3 Viridiplantae kingdom 33090
## 4 Streptophyta phylum 35493
## 5 Streptophytina subphylum 131221
## 6 Embryophyta clade 3193
## 7 Tracheophyta clade 58023
## 8 Euphyllophyta clade 78536
## 9 Spermatophyta clade 58024
## 10 Magnoliopsida class 3398
## 11 Mesangiospermae clade 1437183
## 12 eudicotyledons clade 71240
## 13 Gunneridae clade 91827
## 14 Pentapetalae clade 1437201
## 15 rosids clade 71275
## 16 malvids clade 91836
## 17 Brassicales order 3699
## 18 Brassicaceae family 3700
## 19 Camelineae tribe 980083
## 20 Arabidopsis genus 3701
## 21 Arabidopsis thaliana species 3702The organism argument takes the scientific name of a
query organism, the db argument specifies that database
from which the corresponding taxonomic information shall be retrieved,
e.g. ncbi (NCBI Taxonomy) and itis (Integrated
Taxonomic Information System) and the output argument
specifies the type of taxonomic information that shall be returned for
the query organism, e.g. classification,
taxid, or children.
The output of classification is a
data.frame storing the taxonomic hierarchy of
Arabidopsis thaliana starting with
cellular organisms up to Arabidopsis thaliana.
The first column stores the taxonomic name, the second column the
taxonomic rank, and the third column the NCBI Taxonomy id for
corresponding taxa.
Analogous classification information can be obtained
from different databases.
# retrieving the taxonomic hierarchy of "Arabidopsis thaliana"
# from the Integrated Taxonomic Information System
taxonomy( organism = "Arabidopsis thaliana",
db = "itis",
output = "classification" )Show output
## ══ 1 queries ═══════════════## ✔ Found: Arabidopsis thaliana
## ══ Results ═════════════════
##
## • Total: 1
## • Found: 1
## • Not Found: 0## name rank id
## 1 Plantae kingdom 202422
## 2 Viridiplantae subkingdom 954898
## 3 Streptophyta infrakingdom 846494
## 4 Embryophyta superdivision 954900
## 5 Tracheophyta division 846496
## 6 Spermatophytina subdivision 846504
## 7 Magnoliopsida class 18063
## 8 Rosanae superorder 846548
## 9 Brassicales order 822943
## 10 Brassicaceae family 22669
## 11 Arabidopsis genus 23040
## 12 Arabidopsis thaliana species 23041The output argument allows you to directly access
taxonomy ids for a query organism or species.
retrieve taxonomy ID from ncbi
# retrieving the taxonomy id of the query organism from NCBI Taxonomy
taxonomy( organism = "Arabidopsis thaliana",
db = "ncbi",
output = "taxid" )Show output
## ══ 1 queries ═══════════════## ✔ Found: Arabidopsis+thaliana
## ══ Results ═════════════════
##
## • Total: 1
## • Found: 1
## • Not Found: 0## id
## 1 3702retrieve taxonomy ID from itis
# retrieving the taxonomy id of the query organism from Integrated Taxonomic Information Service
taxonomy( organism = "Arabidopsis",
db = "itis",
output = "taxid" )Show output
## ══ 1 queries ═══════════════## ✔ Found: Arabidopsis
## ══ Results ═════════════════
##
## • Total: 1
## • Found: 1
## • Not Found: 0## id
## 1 23040So far, the following data bases can be accesses to retrieve taxonomic information:
-
db = "itis": Integrated Taxonomic Information Service -
db = "ncbi": National Center for Biotechnology Information
How does the taxonomy(db = "ncbi") output differ
from GenEra?
The taxonomic classifications should be the same between
taxonomy(..., db = "ncbi") and the taxonomic
classifications in the GenEra output (since it uses NCBI
taxdump as input). But it should be noted that the recent updates to
NCBI taxonomy has meant that the highest order ranks (cellular root,
domain, kingdom etc.) may differ.
Retrieve Children Nodes
Another output supported by taxonomy() is
children that returns the immediate children taxa for a
query organism. This feature is useful to determine species
relationships for quantifying recent evolutionary conservation with
Divergence Stratigraphy.
retrieve children nodes from ncbi
# retrieve children taxa of the query organism stored in the correspondning database
taxonomy( organism = "Arabidopsis",
db = "ncbi",
output = "children" )Show output
## ══ 1 queries ═══════════════## ✔ Found: Arabidopsis
## ══ Results ═════════════════
##
## • Total: 1
## • Found: 1
## • Not Found: 0## childtaxa_id
## 1 2608267
## 2 2486701
## 3 1837063
## 4 1547872
## 5 1328956
## 6 1240361
## 7 869751
## 8 869750
## 9 864766
## 10 412662
## 11 378006
## 12 347883
## 13 302551
## 14 97980
## 15 97979
## 16 81970
## 17 59690
## 18 59689
## 19 45251
## 20 45249
## 21 38785
## 22 3702
## childtaxa_name
## 1 Arabidopsis arenosa x Arabidopsis lyrata
## 2 Arabidopsis lyrata x Arabidopsis halleri
## 3 Arabidopsis thaliana x Arabidopsis halleri
## 4 Arabidopsis umezawana
## 5 (Arabidopsis thaliana x Arabidopsis arenosa) x Arabidopsis suecica
## 6 Arabidopsis thaliana x Arabidopsis arenosa
## 7 Arabidopsis thaliana x Arabidopsis halleri subsp. gemmifera
## 8 Arabidopsis thaliana x Arabidopsis lyrata
## 9 Arabidopsis septentrionalis
## 10 Arabidopsis pedemontana
## 11 Arabidopsis arenosa x Arabidopsis thaliana
## 12 Arabidopsis arenicola
## 13 Arabidopsis petrogena
## 14 Arabidopsis croatica
## 15 Arabidopsis cebennensis
## 16 Arabidopsis halleri
## 17 Arabidopsis kamchatica
## 18 Arabidopsis lyrata
## 19 Arabidopsis neglecta
## 20 Arabidopsis suecica
## 21 Arabidopsis arenosa
## 22 Arabidopsis thaliana
## childtaxa_rank
## 1 species
## 2 species
## 3 species
## 4 species
## 5 species
## 6 species
## 7 species
## 8 species
## 9 species
## 10 species
## 11 species
## 12 species
## 13 species
## 14 species
## 15 species
## 16 species
## 17 species
## 18 species
## 19 species
## 20 species
## 21 species
## 22 speciesretrieve children nodes from itis
# retrieve children taxa of the query organism stored in the correspondning database
taxonomy( organism = "Arabidopsis",
db = "itis",
output = "children" )Show output
## ══ 1 queries ═══════════════## ✔ Found: Arabidopsis
## ══ Results ═════════════════
##
## • Total: 1
## • Found: 1
## • Not Found: 0
## ══ 1 queries ═══════════════## ✔ Found: Arabidopsis
## ══ Results ═════════════════
##
## • Total: 1
## • Found: 1
## • Not Found: 0## parentname parenttsn rankname taxonname tsn
## 1 Arabidopsis 23040 Species Arabidopsis arenicola 823113
## 2 Arabidopsis 23040 Species Arabidopsis arenosa 823130
## 3 Arabidopsis 23040 Species Arabidopsis lyrata 823171
## 4 Arabidopsis 23040 Species Arabidopsis thaliana 23041These results allow us to choose subject organisms for
Divergence Stratigraphy.