R/ChebiConn.R
In pkrog/biodbChebi: biodbChebi, a library for connecting to the ChEBI Database
#' ChEBI connector class.
#'
#' This is the connector class for connecting to the ChEBI database through its
#' web services.
#'
#' @examples
#' # Create an instance with default settings:
#' mybiodb <- biodb::newInst()
#'
#' # Create a connector
#' conn <- mybiodb$getFactory()$createConn('chebi')
#'
#' # Get an entry
#' e <- conn$getEntry('15440')
#'
#' # Convert an InChI KEY to a ChEBI identifier
#' conn$convInchiToChebi('YYGNTYWPHWGJRM-AAJYLUCBSA-N')
#'
#' # Terminate instance.
#' mybiodb$terminate()
#'
#' @importFrom R6 R6Class
#' @export
ChebiConn <- R6::R6Class("ChebiConn",
inherit=biodb::BiodbConn,
public=list(
#' @description
#' New instance initializer. Connector classes must not be instantiated
#' directly. Instead, you must use the createConn() method of the factory class.
#' @param ... All parameters are passed to the super class initializer.
#' @return Nothing.
initialize=function(...) {
super$initialize(...)
private$wsdl <- NULL
private$wsValues <- list()
},
#' @description
#' Retrieves the complete WSDL from the web server.
#' @param retfmt The return format to use. 'plain' will return the value as it
#' is returned by the server. 'parsed' will return an XML object. 'request'
#' will return a BiodbRequest object representing the request that would have
#' been sent.
#' @return Depending on `retfmt` value.
wsWsdl=function(retfmt=c('plain', 'parsed', 'request')) {
retfmt <- match.arg(retfmt)
# Build request
url <- c(self$getPropValSlot('urls', 'ws.url'), 'webservice')
request <- self$makeRequest(method='get', url=BiodbUrl$new(url=url,
params='wsdl'))
if (retfmt == 'request')
return(request)
# Send request
results <- self$getBiodb()$getRequestScheduler()$sendRequest(request)
# Parse
if (retfmt == 'parsed')
results <- XML::xmlInternalTreeParse(results, asText=TRUE)
return(results)
},
#' @description
#' Calls getLiteEntity web service and returns the XML result. Be careful when
#' searching by mass (search.category='MASS' or 'MONOISOTOPIC MASS'), since the
#' search is made in text mode, thus the number must be exactly written as it
#' is stored in database, eventually padded with 0 in order to have exactly 5
#' digits after the decimal. An easy solution is to use wildcards to search a
#' mass '410;.718*'.
#' See http //www.ebi.ac.uk/chebi/webServices.do for more details.
#' @param search The text or pattern to search.
#' @param search.category The search category. Call `getSearchCategories()` to
#' get a full list of search categories.
#' @param max.results The maximum of results to return.
#' @param stars How many starts the returned entities should have. Call
#' `getStarsCategories() to get a full list of starts categories.`
#' @param retfmt The return format to use. 'plain' will return the results as
#' given by the server, in a string. 'parsed' will return an XML object.
#' 'request' will return a BiodbRequest object representing the request as
#' would have been sent. 'ids' will return a list of matched entity IDs.
#' @return Depending on `retfmt` value.
wsGetLiteEntity=function(search=NULL, search.category='ALL', stars='ALL',
max.results=10, retfmt=c('plain', 'parsed', 'request', 'ids')) {
retfmt <- match.arg(retfmt)
# Check parameters
chk::chk_string(search)
chk::chk_subset(search.category, self$getSearchCategories())
chk::chk_number(max.results)
chk::chk_gte(max.results, 0)
chk::chk_subset(stars, self$getStarsCategories())
# Build request
params <- c(search=search,
searchCategory=search.category,
maximumResults=max.results,
starsCategory=stars)
url <- c(self$getPropValSlot('urls', 'ws.url'), 'test/getLiteEntity')
request <- self$makeRequest(method='get',
url=BiodbUrl$new(url=url, params=params), encoding='UTF-8')
if (retfmt == 'request')
return(request)
# Send request
results <- self$getBiodb()$getRequestScheduler()$sendRequest(request)
# Parse
if (retfmt != 'plain') {
# Parse XML
results <- XML::xmlInternalTreeParse(results, asText=TRUE)
if (retfmt == 'ids') {
ns <- self$getPropertyValue('xml.ns')
results <- XML::xpathSApply(results, "//chebi:chebiId",
XML::xmlValue, namespaces=ns)
results <- sub('CHEBI:', '', results)
if (length(grep("^[0-9]+$", results)) != length(results))
biodb::error("Impossible to parse XML to get entry IDs.")
}
}
return(results)
},
#' @description
#' Converts a list of IDs (InChI, InChI Keys, CAS, ...) into a list of ChEBI
#' IDs. Several ChEBI IDs may be returned for a single ID.
#' @param ids The identifiers to convert.
#' @param simplify If set to TRUE and only one ChEBI ID has been found for each
#' ID, then a character vector is returned. Otherwise a list of character
#' vectors is returned.
#' @param search.category The search category. Call `getSearchCategories()` to
#' get a full list of search categories.
#' @return Depending on the value of simplify.
convIdsToChebiIds=function(ids, search.category, simplify=TRUE) {
chebi <- list()
msg <- paste('Converting', search.category, 'IDs to ChEBI IDs.')
# Loop on all cas IDs
prg <- biodb::Progress$new(biodb=self$getBiodb(), msg=msg,
total=length(ids))
for (id in ids) {
# Get ChEBI IDs for this ID
if (is.na(id))
x <- character()
else
x <- self$wsGetLiteEntity(id, search.category=search.category,
retfmt='ids')
chebi <- c(chebi, list(x))
# Send progress message
prg$increment()
}
# Simplify
if (simplify && all(vapply(chebi, length, FUN.VALUE=1L) < 2)) {
chebi <- lapply(chebi, function(x) if (length(x) == 0) NA_character_
else x)
chebi <- unlist(chebi)
}
return(chebi)
},
#' @description
#' Converts a list of InChI or InChI KEYs into a list of ChEBI IDs. Several
#' ChEBI IDs may be returned for a single InChI or InChI KEY.
#' @param inchi The InChI values to convert.
#' @param simplify If set to TRUE and only one ChEBI ID has been found for each
#' ID, then a character vector is returned. Otherwise a list of character
#' vectors is returned.
#' @return Depending on the value of simplify.
convInchiToChebi=function(inchi, simplify=TRUE) {
return(self$convIdsToChebiIds(inchi, search.category='INCHI/INCHI KEY',
simplify=simplify))
},
#' @description
#' Converts a list of CAS IDs into a list of ChEBI IDs. Several ChEBI IDs may
#' be returned for a single InChI or InChI KEY.
#' @param cas The CAS IDs to convert.
#' @param simplify If set to TRUE and only one ChEBI ID has been found for each
#' ID, then a character vector is returned. Otherwise a list of character
#' vectors is returned.
#' @return Depending on the value of simplify.
convCasToChebi=function(cas, simplify=TRUE) {
return(self$convIdsToChebiIds(cas, search.category='REGISTRY NUMBERS',
simplify=simplify))
},
#' @description
#' Gets the WSDL as an XML object.
#' @return The ChEBI WSDL as an XML object.
getWsdl=function() {
if (is.null(private$wsdl))
private$wsdl <- self$wsWsdl(retfmt='parsed')
return(private$wsdl)
},
#' @description
#' Extracts a list of values from an enumeration in the WSDL.
#' @param name The name of the enumeration for which to retrieve the values.
#' @return A character vector listing the enumerated values.
getWsdlEnumeration=function(name) {
if ( ! name %in% names(private$wsValues)) {
ns <- self$getPropertyValue('xml.ns')
# Get search categories
expr <- paste0("//xsd:simpleType[@name='", name, "']//xsd:enumeration")
res <- XML::xpathSApply(self$getWsdl(), expr, XML::xmlGetAttr, 'value',
namespaces=ns)
private$wsValues[[name]] <- res
}
return(private$wsValues[[name]])
},
#' @description
#' Gets the list of allowed stars categories for the getLiteEntity web service.
#' @return Returns all the possible stars categories as a character vector.
getStarsCategories=function() {
return(self$getWsdlEnumeration('StarsCategory'))
},
#' @description
#' Gets the list of allowed search categories for the getLiteEntity web
#' service.
#' @return Returns all the possible search categories as a character vector.
getSearchCategories=function() {
return(self$getWsdlEnumeration('SearchCategory'))
}
),
private=list(
wsdl=NULL,
wsValues=NULL,
searchByMass=function(mass.field, mass.min, mass.max, max.results=0) {
ids <- character()
# Set search category
if (mass.field == 'monoisotopic.mass')
search.category <- 'MONOISOTOPIC MASS'
else if (mass.field == 'molecular.mass')
search.category <- 'MASS'
else
biodb::error('Unknown mass field "%s".', mass.field)
# Search for all masses in the range
n <- floor(log10(mass.max - mass.min))
if (n >= 0)
n <- -1
firstMass <- floor(mass.min * 10^-n) * 10^n
lastMass <- ceiling(mass.max * 10^-n) * 10^n
for (m in seq(firstMass, lastMass, 10^n)) {
# Get entries matching integer mass
x <- self$wsGetLiteEntity(search=paste0(m, '*'),
search.category=search.category, max.results=0, retfmt='ids')
# Remove IDs that we already have
x <- x[ ! x %in% ids]
# Filter on mass range
x <- private$filterIdsOnMassRange(x, mass.min, mass.max, mass.field,
max.results - length(ids))
# Add IDs
ids <- c(ids, x)
if ( ! is.na(max.results) && max.results > 0 && length(ids)
>= max.results)
break
}
# Remove duplicates
ids <- ids[ ! duplicated(ids)]
return(ids)
},
doSearchForEntries=function(fields=NULL, max.results=0) {
ids <- NULL
if ( ! is.null(fields)) {
# Search by name
if ('name' %in% names(fields))
ids <- self$wsGetLiteEntity(search=fields$name,
search.category="ALL NAMES", max.results=0, retfmt='ids')
# Search by mass
for (mass.field in c('monoisotopic.mass', 'molecular.mass'))
if (mass.field %in% names(fields)) {
rng <- do.call(Range$new, fields[[mass.field]])
if (is.null(ids))
ids <- private$searchByMass(mass.field,
mass.min=rng$getMin(), mass.max=rng$getMax(),
max.results=max.results)
else
ids <- private$filterIdsOnMassRange(ids,
mass.min=rng$getMin(), mass.max=rng$getMax(),
mass.field=mass.field, limit=max.results)
}
}
return(ids)
},
doGetEntryContentRequest=function(id, concatenate=TRUE) {
url <- c(self$getPropValSlot('urls', 'ws.url'), 'test',
'getCompleteEntity')
urls <- vapply(id, function(x) BiodbUrl$new(url=url,
params=list(chebiId=x))$toString(), FUN.VALUE='')
return(urls)
},
doGetEntryPageUrl=function(id) {
url <- c(self$getPropValSlot('urls', 'base.url'), 'searchId.do')
urls <- vapply(id, function(x) BiodbUrl$new(url=url,
params=list(chebiId=x))$toString(), FUN.VALUE='')
return(urls)
},
doGetEntryImageUrl=function(id) {
url <- c(self$getPropValSlot('urls', 'base.url'), 'displayImage.do')
urls <- vapply(id, function(x) BiodbUrl$new(url=url,
params=list(defaultImage='true', imageIndex=0, chebiId=x,
dimensions=400))$toString(), FUN.VALUE='')
return(urls)
},
doGetEntryIds=function(max.results=NA_integer_) {
return(self$wsGetLiteEntity(search='1*', search.category='CHEBI ID',
max.results=max.results, retfmt='ids'))
},
filterIdsOnMassRange=function(ids, mass.min, mass.max, mass.field, limit=0) {
retids <- character()
msg <- paste0('Filtering ChEBI entries on mass range [', mass.min, ',
', mass.max, '] and field "', mass.field, '".')
# Loop on all IDs
prg <- biodb::Progress$new(biodb=self$getBiodb(), msg=msg,
total=length(ids))
for (id in ids) {
# Print progress
prg$increment()
# Get entry
e <- self$getEntry(id, drop=TRUE)
# Test mass
if ( ! is.null(e)) {
m <- e$getFieldValue(mass.field)
if ( ! is.na(m) && m >= mass.min && m <= mass.max) {
retids <- c(retids, id)
# Stop if limit is reached
if (limit > 0 && length(retids) >= limit)
break
}
}
}
return(retids)
}
))
pkrog/biodbChebi documentation built on March 29, 2022, 8:40 a.m.
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#' ChEBI connector class.
#'
#' This is the connector class for connecting to the ChEBI database through its
#' web services.
#'
#' @examples
#' # Create an instance with default settings:
#' mybiodb <- biodb::newInst()
#'
#' # Create a connector
#' conn <- mybiodb$getFactory()$createConn('chebi')
#'
#' # Get an entry
#' e <- conn$getEntry('15440')
#'
#' # Convert an InChI KEY to a ChEBI identifier
#' conn$convInchiToChebi('YYGNTYWPHWGJRM-AAJYLUCBSA-N')
#'
#' # Terminate instance.
#' mybiodb$terminate()
#'
#' @importFrom R6 R6Class
#' @export
ChebiConn <- R6::R6Class("ChebiConn",
inherit=biodb::BiodbConn,
public=list(
#' @description
#' New instance initializer. Connector classes must not be instantiated
#' directly. Instead, you must use the createConn() method of the factory class.
#' @param ... All parameters are passed to the super class initializer.
#' @return Nothing.
initialize=function(...) {
super$initialize(...)
private$wsdl <- NULL
private$wsValues <- list()
},
#' @description
#' Retrieves the complete WSDL from the web server.
#' @param retfmt The return format to use. 'plain' will return the value as it
#' is returned by the server. 'parsed' will return an XML object. 'request'
#' will return a BiodbRequest object representing the request that would have
#' been sent.
#' @return Depending on `retfmt` value.
wsWsdl=function(retfmt=c('plain', 'parsed', 'request')) {
retfmt <- match.arg(retfmt)
# Build request
url <- c(self$getPropValSlot('urls', 'ws.url'), 'webservice')
request <- self$makeRequest(method='get', url=BiodbUrl$new(url=url,
params='wsdl'))
if (retfmt == 'request')
return(request)
# Send request
results <- self$getBiodb()$getRequestScheduler()$sendRequest(request)
# Parse
if (retfmt == 'parsed')
results <- XML::xmlInternalTreeParse(results, asText=TRUE)
return(results)
},
#' @description
#' Calls getLiteEntity web service and returns the XML result. Be careful when
#' searching by mass (search.category='MASS' or 'MONOISOTOPIC MASS'), since the
#' search is made in text mode, thus the number must be exactly written as it
#' is stored in database, eventually padded with 0 in order to have exactly 5
#' digits after the decimal. An easy solution is to use wildcards to search a
#' mass '410;.718*'.
#' See http //www.ebi.ac.uk/chebi/webServices.do for more details.
#' @param search The text or pattern to search.
#' @param search.category The search category. Call `getSearchCategories()` to
#' get a full list of search categories.
#' @param max.results The maximum of results to return.
#' @param stars How many starts the returned entities should have. Call
#' `getStarsCategories() to get a full list of starts categories.`
#' @param retfmt The return format to use. 'plain' will return the results as
#' given by the server, in a string. 'parsed' will return an XML object.
#' 'request' will return a BiodbRequest object representing the request as
#' would have been sent. 'ids' will return a list of matched entity IDs.
#' @return Depending on `retfmt` value.
wsGetLiteEntity=function(search=NULL, search.category='ALL', stars='ALL',
max.results=10, retfmt=c('plain', 'parsed', 'request', 'ids')) {
retfmt <- match.arg(retfmt)
# Check parameters
chk::chk_string(search)
chk::chk_subset(search.category, self$getSearchCategories())
chk::chk_number(max.results)
chk::chk_gte(max.results, 0)
chk::chk_subset(stars, self$getStarsCategories())
# Build request
params <- c(search=search,
searchCategory=search.category,
maximumResults=max.results,
starsCategory=stars)
url <- c(self$getPropValSlot('urls', 'ws.url'), 'test/getLiteEntity')
request <- self$makeRequest(method='get',
url=BiodbUrl$new(url=url, params=params), encoding='UTF-8')
if (retfmt == 'request')
return(request)
# Send request
results <- self$getBiodb()$getRequestScheduler()$sendRequest(request)
# Parse
if (retfmt != 'plain') {
# Parse XML
results <- XML::xmlInternalTreeParse(results, asText=TRUE)
if (retfmt == 'ids') {
ns <- self$getPropertyValue('xml.ns')
results <- XML::xpathSApply(results, "//chebi:chebiId",
XML::xmlValue, namespaces=ns)
results <- sub('CHEBI:', '', results)
if (length(grep("^[0-9]+$", results)) != length(results))
biodb::error("Impossible to parse XML to get entry IDs.")
}
}
return(results)
},
#' @description
#' Converts a list of IDs (InChI, InChI Keys, CAS, ...) into a list of ChEBI
#' IDs. Several ChEBI IDs may be returned for a single ID.
#' @param ids The identifiers to convert.
#' @param simplify If set to TRUE and only one ChEBI ID has been found for each
#' ID, then a character vector is returned. Otherwise a list of character
#' vectors is returned.
#' @param search.category The search category. Call `getSearchCategories()` to
#' get a full list of search categories.
#' @return Depending on the value of simplify.
convIdsToChebiIds=function(ids, search.category, simplify=TRUE) {
chebi <- list()
msg <- paste('Converting', search.category, 'IDs to ChEBI IDs.')
# Loop on all cas IDs
prg <- biodb::Progress$new(biodb=self$getBiodb(), msg=msg,
total=length(ids))
for (id in ids) {
# Get ChEBI IDs for this ID
if (is.na(id))
x <- character()
else
x <- self$wsGetLiteEntity(id, search.category=search.category,
retfmt='ids')
chebi <- c(chebi, list(x))
# Send progress message
prg$increment()
}
# Simplify
if (simplify && all(vapply(chebi, length, FUN.VALUE=1L) < 2)) {
chebi <- lapply(chebi, function(x) if (length(x) == 0) NA_character_
else x)
chebi <- unlist(chebi)
}
return(chebi)
},
#' @description
#' Converts a list of InChI or InChI KEYs into a list of ChEBI IDs. Several
#' ChEBI IDs may be returned for a single InChI or InChI KEY.
#' @param inchi The InChI values to convert.
#' @param simplify If set to TRUE and only one ChEBI ID has been found for each
#' ID, then a character vector is returned. Otherwise a list of character
#' vectors is returned.
#' @return Depending on the value of simplify.
convInchiToChebi=function(inchi, simplify=TRUE) {
return(self$convIdsToChebiIds(inchi, search.category='INCHI/INCHI KEY',
simplify=simplify))
},
#' @description
#' Converts a list of CAS IDs into a list of ChEBI IDs. Several ChEBI IDs may
#' be returned for a single InChI or InChI KEY.
#' @param cas The CAS IDs to convert.
#' @param simplify If set to TRUE and only one ChEBI ID has been found for each
#' ID, then a character vector is returned. Otherwise a list of character
#' vectors is returned.
#' @return Depending on the value of simplify.
convCasToChebi=function(cas, simplify=TRUE) {
return(self$convIdsToChebiIds(cas, search.category='REGISTRY NUMBERS',
simplify=simplify))
},
#' @description
#' Gets the WSDL as an XML object.
#' @return The ChEBI WSDL as an XML object.
getWsdl=function() {
if (is.null(private$wsdl))
private$wsdl <- self$wsWsdl(retfmt='parsed')
return(private$wsdl)
},
#' @description
#' Extracts a list of values from an enumeration in the WSDL.
#' @param name The name of the enumeration for which to retrieve the values.
#' @return A character vector listing the enumerated values.
getWsdlEnumeration=function(name) {
if ( ! name %in% names(private$wsValues)) {
ns <- self$getPropertyValue('xml.ns')
# Get search categories
expr <- paste0("//xsd:simpleType[@name='", name, "']//xsd:enumeration")
res <- XML::xpathSApply(self$getWsdl(), expr, XML::xmlGetAttr, 'value',
namespaces=ns)
private$wsValues[[name]] <- res
}
return(private$wsValues[[name]])
},
#' @description
#' Gets the list of allowed stars categories for the getLiteEntity web service.
#' @return Returns all the possible stars categories as a character vector.
getStarsCategories=function() {
return(self$getWsdlEnumeration('StarsCategory'))
},
#' @description
#' Gets the list of allowed search categories for the getLiteEntity web
#' service.
#' @return Returns all the possible search categories as a character vector.
getSearchCategories=function() {
return(self$getWsdlEnumeration('SearchCategory'))
}
),
private=list(
wsdl=NULL,
wsValues=NULL,
searchByMass=function(mass.field, mass.min, mass.max, max.results=0) {
ids <- character()
# Set search category
if (mass.field == 'monoisotopic.mass')
search.category <- 'MONOISOTOPIC MASS'
else if (mass.field == 'molecular.mass')
search.category <- 'MASS'
else
biodb::error('Unknown mass field "%s".', mass.field)
# Search for all masses in the range
n <- floor(log10(mass.max - mass.min))
if (n >= 0)
n <- -1
firstMass <- floor(mass.min * 10^-n) * 10^n
lastMass <- ceiling(mass.max * 10^-n) * 10^n
for (m in seq(firstMass, lastMass, 10^n)) {
# Get entries matching integer mass
x <- self$wsGetLiteEntity(search=paste0(m, '*'),
search.category=search.category, max.results=0, retfmt='ids')
# Remove IDs that we already have
x <- x[ ! x %in% ids]
# Filter on mass range
x <- private$filterIdsOnMassRange(x, mass.min, mass.max, mass.field,
max.results - length(ids))
# Add IDs
ids <- c(ids, x)
if ( ! is.na(max.results) && max.results > 0 && length(ids)
>= max.results)
break
}
# Remove duplicates
ids <- ids[ ! duplicated(ids)]
return(ids)
},
doSearchForEntries=function(fields=NULL, max.results=0) {
ids <- NULL
if ( ! is.null(fields)) {
# Search by name
if ('name' %in% names(fields))
ids <- self$wsGetLiteEntity(search=fields$name,
search.category="ALL NAMES", max.results=0, retfmt='ids')
# Search by mass
for (mass.field in c('monoisotopic.mass', 'molecular.mass'))
if (mass.field %in% names(fields)) {
rng <- do.call(Range$new, fields[[mass.field]])
if (is.null(ids))
ids <- private$searchByMass(mass.field,
mass.min=rng$getMin(), mass.max=rng$getMax(),
max.results=max.results)
else
ids <- private$filterIdsOnMassRange(ids,
mass.min=rng$getMin(), mass.max=rng$getMax(),
mass.field=mass.field, limit=max.results)
}
}
return(ids)
},
doGetEntryContentRequest=function(id, concatenate=TRUE) {
url <- c(self$getPropValSlot('urls', 'ws.url'), 'test',
'getCompleteEntity')
urls <- vapply(id, function(x) BiodbUrl$new(url=url,
params=list(chebiId=x))$toString(), FUN.VALUE='')
return(urls)
},
doGetEntryPageUrl=function(id) {
url <- c(self$getPropValSlot('urls', 'base.url'), 'searchId.do')
urls <- vapply(id, function(x) BiodbUrl$new(url=url,
params=list(chebiId=x))$toString(), FUN.VALUE='')
return(urls)
},
doGetEntryImageUrl=function(id) {
url <- c(self$getPropValSlot('urls', 'base.url'), 'displayImage.do')
urls <- vapply(id, function(x) BiodbUrl$new(url=url,
params=list(defaultImage='true', imageIndex=0, chebiId=x,
dimensions=400))$toString(), FUN.VALUE='')
return(urls)
},
doGetEntryIds=function(max.results=NA_integer_) {
return(self$wsGetLiteEntity(search='1*', search.category='CHEBI ID',
max.results=max.results, retfmt='ids'))
},
filterIdsOnMassRange=function(ids, mass.min, mass.max, mass.field, limit=0) {
retids <- character()
msg <- paste0('Filtering ChEBI entries on mass range [', mass.min, ',
', mass.max, '] and field "', mass.field, '".')
# Loop on all IDs
prg <- biodb::Progress$new(biodb=self$getBiodb(), msg=msg,
total=length(ids))
for (id in ids) {
# Print progress
prg$increment()
# Get entry
e <- self$getEntry(id, drop=TRUE)
# Test mass
if ( ! is.null(e)) {
m <- e$getFieldValue(mass.field)
if ( ! is.na(m) && m >= mass.min && m <= mass.max) {
retids <- c(retids, id)
# Stop if limit is reached
if (limit > 0 && length(retids) >= limit)
break
}
}
}
return(retids)
}
))
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Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.