Nothing
R/slinky_clue.R
In slinky: Putting the fun in LINCS L1000 data analysis
Defines functions
.checkClue
# sanity check
.checkClue = function() {
res <- httr::GET(url = "clue.io/api")
grepl("API Access", httr::content(res, as = "text"))
}
#' clue
#'
#' Wrapper for clue.io REST calls
#'
#' @param x a Slinky Object
#' @param endpoint The endpoint to query. Default is 'sigs'.
#' @param fields Optional vector of fields to return.
#' @param where_clause Optional where_clause clause. Must be
#' named list (e.g. list(field='value')
#' @param ids Optional vector of ids to fetch for sigs or profiles
#' endpoints. Should not be used together with where_clause or
#' count.
#' @param unpack_sigs The sigs endpoint returns multiple
#' distil_ids per row. Should we unpack these to one per row?
#' @param poscon Instances of type \code{trt_poscon} are recoded
#' as \code{trt_cp} in clue.io's \code{sigs} endpoint.
#' This can lead to unexpected results downstream. To keep these
#' instances, specify \code{poscon='keep'}
#' @param limit Optional limit to number of instances (samples to return
#' @param count Should we just return the count of intances satisfying
#' the query rather than the data? Default is FALSE.
#' @param cl Optional cluster object to parallelize this
#' operation. If verbose is TRUE, use this pattern in order for
#' progress bar to update:
#' \code{cl <- parallel::makeCluster(4, outfile=\"\")}
#' @param verbose Do you want to know how things are going?
#' Default is false.
#' @return Data returned by Slinky.api as a data.frame
#' @name clue
#' @rdname clue
#' @import foreach
#' @importFrom dplyr %>% mutate
#' @importFrom tidyr unnest
#' @importFrom httr GET
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
setGeneric("clue",
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
fields = "",
where_clause = NULL,
ids = NULL,
limit = 0,
count = FALSE,
unpack_sigs = TRUE,
poscon = c("omit", "keep"),
cl = NULL,
verbose = FALSE) {
standardGeneric("clue")
}
)
#' @rdname clue
#' @exportMethod clue
#' @importFrom dplyr bind_rows %>%
#' @aliases clue,Slinky-method
setMethod("clue", signature(x = "Slinky"),
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
fields = "",
where_clause = NULL,
ids = NULL,
limit = 0,
count = FALSE,
unpack_sigs = TRUE,
poscon = c("omit", "keep"),
cl = NULL,
verbose = FALSE)
{
if (!.checkClue()) {
stop("Could not connect to clue.io APi. Please verify connecivity.")
}
if (sum(length(ids) & count & length(where_clause)) > 1) {
stop(
"In call to Slinky$clue, the ids, where_clause, and count arguments
are mutually exclusive. Ensure only 1 provided."
)
}
if (length(ids) && !endpoint %in% c("sigs", "profiles")) {
stop("Specifying id list currently only supported for sigs and ",
"profiles endpoints")
}
endpoint <- match.arg(endpoint)
poscon <- match.arg(poscon)
key <- x@user_key
base <- x@base
if (count) {
return(clueCount(x, endpoint, where_clause))
} else {
if (length(ids)) {
count <- length(ids)
} else {
count <- clueCount(x, endpoint, where_clause)
}
}
if (count == 0)
return(NULL)
if (limit > 0) {
count <- min(limit, count)
} else {
limit <- count
}
if (length(cl)) {
doParallel::registerDoParallel(cl)
} else {
foreach::registerDoSEQ()
}
# we cannot retrieve more than 1000 records at a time, nor can we send
# more than 1000 ids in an inq statement so throttle to 1000 records per
# request, unless user has requested fewer
if (limit < 1000) {
lim_filter <- limit
} else {
lim_filter <- 1000
}
if (verbose) {
message("Retrieving metadata from clue.io")
pb <- txtProgressBar(
min = 0,
max = ceiling(count / 1000),
initial = 0,
width = 100,
style = 3
)
}
if (poscon == "omit") {
pc <- readRDS(system.file("extdata", "trt_poscon.rds",
package = "slinky"))
}
i <- 0 # keep R CHECK happy.
dat <- foreach(
i = seq_len(ceiling(count / 1000)),
.combine = dplyr::bind_rows,
.export = c("x"),
.packages = c("httr", "jsonlite")) %dopar% {
if (verbose) {
utils::setTxtProgressBar(pb, i)
}
if (i * 1000 > limit) {
lim_filter <- limit %% 1000
}
ii <- (i - 1) * 1000
if (length(ids)) {
where_clause = list("distil_id" =
list(inq = c(ids[seq(ii, ii + lim_filter)])))
skip <- 0
} else {
skip <- ii
}
if (poscon == "omit") {
ix <- which(ids %in% pc$distil_id)
if (length(ix)) {
ids <- ids[-ix]
}
}
res <- httr::GET(
url = x@base,
path = paste0("api/", endpoint, "/"),
query = list(
filter = jsonlite::toJSON(
list(
fields = fields,
limit = lim_filter,
where = where_clause,
skip = skip
),
auto_unbox = TRUE
),
user_key = key
)
)
# flatten the data structures to 2D
fl <- lapply(httr::content(res, as = "parsed"),
function(x) {
lapply(x, unlist)
})
fl <- lapply(fl, function(x) {
lapply(x, paste, collapse = "|")
})
dplyr::bind_rows(lapply(fl,
as.data.frame,
stringsAsFactors = FALSE))
}
if (length(dat) == 0) {
return(NULL)
}
if (endpoint == "sigs" && unpack_sigs) {
distil_id <- NULL # prevent "no visible binding" on R CMD CHECK
dat <- dat %>%
mutate("distil_id" = strsplit(distil_id, "\\|")) %>%
unnest(distil_id)
}
dat
})
#' clueVehicle
#'
#' Fetch the vehicle control applicable to given ids (distil_id). Expects
#' that perturbagen is of type trt_cp.
#'
#' @param x a Slinky Object
#' @param ids The distil_id(s) to lookup.
#' @param verbose Do you want to know how things are going?
#' Default is FALSE.
#' @return The name of the vehicle control for the queried
#' perturbagen(s).
#' This is a convenience wrapper to the profiles API
#' which queries clue.io and unwraps response.
#' @name clueVehicle
#' @rdname clueVehicle
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
#' amox.ctrl <- clueVehicle(sl, amox$distil_id)
#'
setGeneric("clueVehicle",
function(x, ids, verbose = FALSE) {
standardGeneric("clueVehicle")
}
)
#' @rdname clueVehicle
#' @exportMethod clueVehicle
#' @aliases clueVehicle
setMethod("clueVehicle", signature(x = "Slinky"),
function(x, ids, verbose = FALSE)
{
if (length(ids) > 1) {
where_clause = list(distil_id = list(inq = c(ids)))
} else {
where_clause = list(distil_id = ids)
}
res <- clue(x,
"profiles",
fields = c("pert_id",
"pert_iname", "pert_vehicle"),
where_clause = where_clause,
verbose = verbose
)
return(res)
})
#' clueInstances
#'
#' Convenience wrapper to query function to retrieve instance ids meeting
#' specified criteria.
#'
#' @param x a Slinky Object
#' @param where_clause Filter terms, as a list of terms, e.g.
#' \code{list(pert_type='trt_cp', 'is_gold'=TRUE)}. Terms will be
#' joined by AND logic.
#' @param verbose Do you want to know how things are going?
#' Default is false.
#' @param poscon Instances of type \code{trt_poscon} are recoded
#' as \code{trt_cp} in clue.io's \code{sigs} endpoint.
#' This can lead to unexpected results downstream. To keep these
#' instances, specify \code{poscon='keep'}
#' @return Vector of ids matching criteria.
#' This is a convenience wrapper to the signature API
#' which queries clue.io and unwraps response.
#' @name clueInstances
#' @rdname clueInstances
setGeneric("clueInstances",
function(x, where_clause = NULL,
verbose = FALSE,
poscon = c("omit", "keep")) {
standardGeneric("clueInstances")
}
)
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox_ids <- clueInstances(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
#'
#' @rdname clueInstances
#' @exportMethod clueInstances
#' @aliases clueInstances
setMethod("clueInstances", signature(x = "Slinky"),
function(x, where_clause = NULL,
verbose = FALSE,
poscon = c("omit", "keep"))
{
if (!length(where_clause) && !length(ids)) {
stop("The 'where_clause' argument must be specified.")
}
poscon = match.arg(poscon)
ids <- clue(x,
"sigs",
fields = c("distil_id"),
where_clause = where_clause,
unpack_sigs = TRUE,
verbose = verbose
)
ids <- as.character(unlist(vapply(ids[, 1], function(x) {
list(strsplit(x, "\\|"))
}, list("a"))))
if (poscon == "omit") {
pc <- readRDS(system.file("extdata", "trt_poscon.rds",
package = "slinky"))
ix <- which(ids %in% pc$distil_id)
if (length(ix)) {
ids <- ids[-ix]
}
}
ids
})
#' clueCount
#'
#' Wrapper for Slinky.io REST calls to retrieve record counts
#'
#' @param x a Slinky Object
#' @param endpoint The endpoint to query, default is 'sigs'.
#' @param where_clause Optional where_clause clause. Must be
#' named list (e.g. list(field='value')
#' @return Count of records satisfying query
#' @name clueCount
#' @rdname clueCount
setGeneric("clueCount",
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
where_clause = "") {
standardGeneric("clueCount")
}
)
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox_count <- clueCount(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
#'
#' @rdname clueCount
#' @exportMethod clueCount
#' @aliases clueCount
setMethod("clueCount", signature(x = "Slinky"),
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
where_clause = "")
{
endpoint = match.arg(endpoint)
key <- x@user_key
base <- x@base
if (is(where_clause, "list")) {
query = list(
where = jsonlite::toJSON(where_clause,
auto_unbox = TRUE),
user_key = key
)
} else {
query = list(user_key = key)
}
# https://api.clue.io/api/rep_drugs/count?where=%7B%22pert_iname%22%3A%22tacrolimus%22%7D&user_key=MYSUSERKEY
res <- httr::GET(
url = base,
path = paste0("api/", endpoint, "/count"),
query = query
)
res <- httr::content(res)
if (length(res$error)) {
stop("Call to clue.io API returned this error: ", res$error)
}
count <- res$count
if (!length(count)) {
count <- 0
}
return(count)
})
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Defines functions .checkClue
# sanity check
.checkClue = function() {
res <- httr::GET(url = "clue.io/api")
grepl("API Access", httr::content(res, as = "text"))
}
#' clue
#'
#' Wrapper for clue.io REST calls
#'
#' @param x a Slinky Object
#' @param endpoint The endpoint to query. Default is 'sigs'.
#' @param fields Optional vector of fields to return.
#' @param where_clause Optional where_clause clause. Must be
#' named list (e.g. list(field='value')
#' @param ids Optional vector of ids to fetch for sigs or profiles
#' endpoints. Should not be used together with where_clause or
#' count.
#' @param unpack_sigs The sigs endpoint returns multiple
#' distil_ids per row. Should we unpack these to one per row?
#' @param poscon Instances of type \code{trt_poscon} are recoded
#' as \code{trt_cp} in clue.io's \code{sigs} endpoint.
#' This can lead to unexpected results downstream. To keep these
#' instances, specify \code{poscon='keep'}
#' @param limit Optional limit to number of instances (samples to return
#' @param count Should we just return the count of intances satisfying
#' the query rather than the data? Default is FALSE.
#' @param cl Optional cluster object to parallelize this
#' operation. If verbose is TRUE, use this pattern in order for
#' progress bar to update:
#' \code{cl <- parallel::makeCluster(4, outfile=\"\")}
#' @param verbose Do you want to know how things are going?
#' Default is false.
#' @return Data returned by Slinky.api as a data.frame
#' @name clue
#' @rdname clue
#' @import foreach
#' @importFrom dplyr %>% mutate
#' @importFrom tidyr unnest
#' @importFrom httr GET
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
setGeneric("clue",
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
fields = "",
where_clause = NULL,
ids = NULL,
limit = 0,
count = FALSE,
unpack_sigs = TRUE,
poscon = c("omit", "keep"),
cl = NULL,
verbose = FALSE) {
standardGeneric("clue")
}
)
#' @rdname clue
#' @exportMethod clue
#' @importFrom dplyr bind_rows %>%
#' @aliases clue,Slinky-method
setMethod("clue", signature(x = "Slinky"),
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
fields = "",
where_clause = NULL,
ids = NULL,
limit = 0,
count = FALSE,
unpack_sigs = TRUE,
poscon = c("omit", "keep"),
cl = NULL,
verbose = FALSE)
{
if (!.checkClue()) {
stop("Could not connect to clue.io APi. Please verify connecivity.")
}
if (sum(length(ids) & count & length(where_clause)) > 1) {
stop(
"In call to Slinky$clue, the ids, where_clause, and count arguments
are mutually exclusive. Ensure only 1 provided."
)
}
if (length(ids) && !endpoint %in% c("sigs", "profiles")) {
stop("Specifying id list currently only supported for sigs and ",
"profiles endpoints")
}
endpoint <- match.arg(endpoint)
poscon <- match.arg(poscon)
key <- x@user_key
base <- x@base
if (count) {
return(clueCount(x, endpoint, where_clause))
} else {
if (length(ids)) {
count <- length(ids)
} else {
count <- clueCount(x, endpoint, where_clause)
}
}
if (count == 0)
return(NULL)
if (limit > 0) {
count <- min(limit, count)
} else {
limit <- count
}
if (length(cl)) {
doParallel::registerDoParallel(cl)
} else {
foreach::registerDoSEQ()
}
# we cannot retrieve more than 1000 records at a time, nor can we send
# more than 1000 ids in an inq statement so throttle to 1000 records per
# request, unless user has requested fewer
if (limit < 1000) {
lim_filter <- limit
} else {
lim_filter <- 1000
}
if (verbose) {
message("Retrieving metadata from clue.io")
pb <- txtProgressBar(
min = 0,
max = ceiling(count / 1000),
initial = 0,
width = 100,
style = 3
)
}
if (poscon == "omit") {
pc <- readRDS(system.file("extdata", "trt_poscon.rds",
package = "slinky"))
}
i <- 0 # keep R CHECK happy.
dat <- foreach(
i = seq_len(ceiling(count / 1000)),
.combine = dplyr::bind_rows,
.export = c("x"),
.packages = c("httr", "jsonlite")) %dopar% {
if (verbose) {
utils::setTxtProgressBar(pb, i)
}
if (i * 1000 > limit) {
lim_filter <- limit %% 1000
}
ii <- (i - 1) * 1000
if (length(ids)) {
where_clause = list("distil_id" =
list(inq = c(ids[seq(ii, ii + lim_filter)])))
skip <- 0
} else {
skip <- ii
}
if (poscon == "omit") {
ix <- which(ids %in% pc$distil_id)
if (length(ix)) {
ids <- ids[-ix]
}
}
res <- httr::GET(
url = x@base,
path = paste0("api/", endpoint, "/"),
query = list(
filter = jsonlite::toJSON(
list(
fields = fields,
limit = lim_filter,
where = where_clause,
skip = skip
),
auto_unbox = TRUE
),
user_key = key
)
)
# flatten the data structures to 2D
fl <- lapply(httr::content(res, as = "parsed"),
function(x) {
lapply(x, unlist)
})
fl <- lapply(fl, function(x) {
lapply(x, paste, collapse = "|")
})
dplyr::bind_rows(lapply(fl,
as.data.frame,
stringsAsFactors = FALSE))
}
if (length(dat) == 0) {
return(NULL)
}
if (endpoint == "sigs" && unpack_sigs) {
distil_id <- NULL # prevent "no visible binding" on R CMD CHECK
dat <- dat %>%
mutate("distil_id" = strsplit(distil_id, "\\|")) %>%
unnest(distil_id)
}
dat
})
#' clueVehicle
#'
#' Fetch the vehicle control applicable to given ids (distil_id). Expects
#' that perturbagen is of type trt_cp.
#'
#' @param x a Slinky Object
#' @param ids The distil_id(s) to lookup.
#' @param verbose Do you want to know how things are going?
#' Default is FALSE.
#' @return The name of the vehicle control for the queried
#' perturbagen(s).
#' This is a convenience wrapper to the profiles API
#' which queries clue.io and unwraps response.
#' @name clueVehicle
#' @rdname clueVehicle
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
#' amox.ctrl <- clueVehicle(sl, amox$distil_id)
#'
setGeneric("clueVehicle",
function(x, ids, verbose = FALSE) {
standardGeneric("clueVehicle")
}
)
#' @rdname clueVehicle
#' @exportMethod clueVehicle
#' @aliases clueVehicle
setMethod("clueVehicle", signature(x = "Slinky"),
function(x, ids, verbose = FALSE)
{
if (length(ids) > 1) {
where_clause = list(distil_id = list(inq = c(ids)))
} else {
where_clause = list(distil_id = ids)
}
res <- clue(x,
"profiles",
fields = c("pert_id",
"pert_iname", "pert_vehicle"),
where_clause = where_clause,
verbose = verbose
)
return(res)
})
#' clueInstances
#'
#' Convenience wrapper to query function to retrieve instance ids meeting
#' specified criteria.
#'
#' @param x a Slinky Object
#' @param where_clause Filter terms, as a list of terms, e.g.
#' \code{list(pert_type='trt_cp', 'is_gold'=TRUE)}. Terms will be
#' joined by AND logic.
#' @param verbose Do you want to know how things are going?
#' Default is false.
#' @param poscon Instances of type \code{trt_poscon} are recoded
#' as \code{trt_cp} in clue.io's \code{sigs} endpoint.
#' This can lead to unexpected results downstream. To keep these
#' instances, specify \code{poscon='keep'}
#' @return Vector of ids matching criteria.
#' This is a convenience wrapper to the signature API
#' which queries clue.io and unwraps response.
#' @name clueInstances
#' @rdname clueInstances
setGeneric("clueInstances",
function(x, where_clause = NULL,
verbose = FALSE,
poscon = c("omit", "keep")) {
standardGeneric("clueInstances")
}
)
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox_ids <- clueInstances(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
#'
#' @rdname clueInstances
#' @exportMethod clueInstances
#' @aliases clueInstances
setMethod("clueInstances", signature(x = "Slinky"),
function(x, where_clause = NULL,
verbose = FALSE,
poscon = c("omit", "keep"))
{
if (!length(where_clause) && !length(ids)) {
stop("The 'where_clause' argument must be specified.")
}
poscon = match.arg(poscon)
ids <- clue(x,
"sigs",
fields = c("distil_id"),
where_clause = where_clause,
unpack_sigs = TRUE,
verbose = verbose
)
ids <- as.character(unlist(vapply(ids[, 1], function(x) {
list(strsplit(x, "\\|"))
}, list("a"))))
if (poscon == "omit") {
pc <- readRDS(system.file("extdata", "trt_poscon.rds",
package = "slinky"))
ix <- which(ids %in% pc$distil_id)
if (length(ix)) {
ids <- ids[-ix]
}
}
ids
})
#' clueCount
#'
#' Wrapper for Slinky.io REST calls to retrieve record counts
#'
#' @param x a Slinky Object
#' @param endpoint The endpoint to query, default is 'sigs'.
#' @param where_clause Optional where_clause clause. Must be
#' named list (e.g. list(field='value')
#' @return Count of records satisfying query
#' @name clueCount
#' @rdname clueCount
setGeneric("clueCount",
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
where_clause = "") {
standardGeneric("clueCount")
}
)
#' @examples
#' # for build/demo only. You MUST use your own key when using the slinky
#' # package.
#' user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
#' as='parsed')$user_key
#' sl <- Slinky(user_key,
#' system.file('extdata', 'demo.gctx',
#' package='slinky'),
#' system.file('extdata', 'demo_inst_info.txt',
#' package = 'slinky'))
#' amox_count <- clueCount(sl, where_clause = list("pert_iname" = "amoxicillin",
#' "cell_id" = "MCF7",
#' "is_gold" = TRUE))
#'
#' @rdname clueCount
#' @exportMethod clueCount
#' @aliases clueCount
setMethod("clueCount", signature(x = "Slinky"),
function(x, endpoint = c("sigs",
"cells",
"genes",
"perts",
"plates",
"profiles",
"rep_drugs",
"rep_drug_indications",
"pcls"),
where_clause = "")
{
endpoint = match.arg(endpoint)
key <- x@user_key
base <- x@base
if (is(where_clause, "list")) {
query = list(
where = jsonlite::toJSON(where_clause,
auto_unbox = TRUE),
user_key = key
)
} else {
query = list(user_key = key)
}
# https://api.clue.io/api/rep_drugs/count?where=%7B%22pert_iname%22%3A%22tacrolimus%22%7D&user_key=MYSUSERKEY
res <- httr::GET(
url = base,
path = paste0("api/", endpoint, "/count"),
query = query
)
res <- httr::content(res)
if (length(res$error)) {
stop("Call to clue.io API returned this error: ", res$error)
}
count <- res$count
if (!length(count)) {
count <- 0
}
return(count)
})
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