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#' @name HCAMatrix-class
#' @title A class for representing the HCAMatrix API
#'
#' @description The `HCAMatrix` class is a representation of the `HCAMatrix`
#' API protocol via OAS version 2.0. The original version OAS 3 was converted
#' using the APIMatic converter (\url{apimatic.io}).
#'
#' @importFrom methods new slot slot<-
#'
#' @seealso \link{HCAMatrix}, \link[AnVIL]{Service}
#'
#' @examples
#'
#' HCAMatrix()
#'
#' @export
.HCAMatrix <- setClass("HCAMatrix", contains = "Service",
representation(filter = "list"))
#' @rdname HCAMatrix
#'
#' @aliases HCAMatrix
#'
#' @title API Entry function for the Human Cell Atlas Matrix service
#'
#' @description This function allows the use of the HCA Matrix API
#'
#' @param api An HCAMatrix API object
#'
#' @param filter_name character(1) The name of the filter to get more detail on
#'
#' @param format_name character(1) The format for which to obtain more detail on
#'
#' @param feature_name character(1) The feature for which to obtain more detail
#' on
#'
#' @return An object of class 'HCAMatrix'
#'
#' @importFrom AnVIL Service
#'
#' @examples
#' hca <- HCAMatrix()
#'
#' @export
HCAMatrix <- function() {
.HCAMatrix(
Service(
service = "HCAMatrix",
host = "matrix.data.humancellatlas.org",
config = httr::config(ssl_verifypeer = 0L, ssl_verifyhost = 0L,
http_version = 0L),
authenticate = FALSE,
api_url =
system.file("service/swagger.yaml",
package = "HCAMatrixBrowser", mustWork = TRUE),
package = "HCAMatrixBrowser",
schemes = "https"
)
)
}
#' @name HCAMatrix
#'
#' @section Filters:
#' * available_filter - Get a list of filters within the API to filter with
#' * filter_detail - Obtain more detail on a particular filter name
#'
#' @export
available_filters <- function(api) {
unlist(
httr::content(
api$matrix.lambdas.api.v1.core.get_filters()
)
)
}
#' @name HCAMatrix
#'
#' @export
filter_detail <- function(api, filter_name) {
stopifnot(is.character(filter_name), length(filter_name) == 1L,
!is.na(filter_name), !is.logical(filter_name))
httr::content(
api$matrix.lambdas.api.v1.core.get_filter_detail(
filter_name = filter_name
)
)
}
#' @name HCAMatrix
#'
#' @section Formats:
#' * available_formats - Get a list of matrix format outputs
#' * format_detail - Obtain more detail on a particular matrix file format
#'
#' @export
available_formats <- function(api) {
unlist(
httr::content(
api$matrix.lambdas.api.v0.core.get_formats()
)
)
}
#' @name HCAMatrix
#'
#' @export
format_detail <- function(api, format_name) {
stopifnot(is.character(format_name), length(format_name) == 1L,
!is.na(format_name), !is.logical(format_name))
temphtml <- tempfile(fileext = ".html")
writeLines(
httr::content(
api$matrix.lambdas.api.v1.core.get_format_detail(
format_name = format_name
)
), con = file(temphtml)
)
utils::browseURL(temphtml)
}
#' @name HCAMatrix
#'
#' @section Features:
#' * available_features - Get a list of feature outputs, either genes or
#' transcripts
#' * feature_detail - Obtain more information on a matrix feature type
#'
#' @export
available_features <- function(api) {
unlist(
httr::content(
api$matrix.lambdas.api.v1.core.get_features()
)
)
}
#' @name HCAMatrix
#'
#' @export
feature_detail <- function(api, feature_name) {
httr::content(
api$matrix.lambdas.api.v1.core.get_feature_detail(
feature_name = feature_name
)
)
}
#' @name filtering
#'
#' @aliases filter filters
#'
#' @title Manipulating HCAMatrix filters
#'
#' @return A \code{\link{HCAMatrix}} object with the filter
#' field replaced by the specified filter expression
#'
#' @examples
#' # make an HCAMatrix object to start
#' hca <- HCAMatrix()
#'
#' head(available_filters(hca))
#'
#' hca1 <- filter(hca, genes_detected >= 500)
#' filters(hca1)
#'
#' @section filter:
#' The \code{filter} is a convenient setter for the filter
#' element in \code{\link{HCAMatrix}} objects.
#' @section filters:
#' The \code{filters} (plural) function is a safe accessor for the filters
#' already present in the `HCAMAtrix` API object. The filter can also be
#' set using the `filters<-` function setter (advanced use).
#'
#' @param x the object on which to set the filter list
#' member
#'
#' @param expr a filter expression in the form of
#' the right hand side of a formula, where bare names
#' (without quotes) are allowed if they are available
#' fields associated with the HCAMAtrix object, \code{x}
#'
#' @param value A list of structured filters (internal use)
#'
#' @note Filtering documentation provided by the `GenomicDataCommons` package
#'
#' @export
setGeneric("filter", function(x, expr) { standardGeneric("filter") })
#' @rdname filtering
#'
#' @export
setGeneric("filters", function(x) { standardGeneric("filters") })
#' @rdname filtering
#'
#' @export
setGeneric("filters<-", function(x, value) { standardGeneric("filters<-") })
#' @rdname filtering
#'
#' @export
setMethod("filter", c("HCAMatrix", "ANY"), function(x, expr) {
filt <- try({
if (rlang::is_formula(expr))
make_filter(expr, available_filters(x))
}, silent = TRUE)
if (inherits(filt, "try-error"))
filt <- make_filter(rlang::enquo(expr), available_filters(x))
filters(x) <- filt
x
})
#' @rdname filtering
#'
#' @exportMethod filters
setMethod("filters", "HCAMatrix", function(x) {
x@filter
})
.replaceSlots <-
function (object, ..., .slotList = list())
{
slots <- c(list(...), .slotList)
slots_names <- names(slots)
for (i in seq_along(slots)) {
slot_name <- slots_names[[i]]
if (slot_name == "mcols")
slot_name <- "elementMetadata"
old_slot_val <- slot(object, slot_name)
slot_val <- slots[[i]]
slot(object, slot_name, check = FALSE) <- slot_val
}
object
}
#' @rdname filtering
#'
#' @export
setReplaceMethod("filters", c("HCAMatrix", "ANY"), function(x, value) {
current <- filters(x)
if (length(current))
.replaceSlots(
x,
filter = list(op = "and", value = list(current, value))
)
else
.replaceSlots(x, filter = value)
})
make_filter <- function(expr, available_filters) {
afilters <- stats::setNames(available_filters, available_filters)
filterlist <- c(.oplookup, afilters)
if (rlang::is_formula(expr))
rlang::eval_tidy(rlang::f_rhs(expr), data = filterlist,
env = rlang::f_env(expr))
else
rlang::eval_tidy(expr, data = filterlist)
}
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