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#' @name SpatialExperiment-subset
#'
#' @title Subsetting SpatialExperiment objects
#'
#' @aliases [,SpatialExperiment,ANY,ANY,ANY-method
#'
#' @description
#' The subsetting method for \code{\link{SpatialExperiment}} objects ensures
#' that spatial data attributes (\code{\link{spatialCoords}} and
#' \code{\link{imgData}}) are subsetted correctly to match rows and columns with
#' the remainder of the object.
#'
#' @section subset:
#' \describe{
#' \item{\code{[}:}{ subsetting method}
#' }
#'
#' @param x a \code{\link{SpatialExperiment}} object
#' @param i row indices for subsetting
#' @param j column indices for subsetting
#'
#' @return a \code{\link{SpatialExperiment}} object
#'
#' @examples
#' example(read10xVisium)
#'
#' dim(spe)
#'
#' set.seed(123)
#' idx <- sample(ncol(spe), 10)
#' sub <- spe[, idx]
#' dim(sub)
#' colData(sub)
#' spatialCoords(sub)
NULL
# we overwrite the default subsetting method
# to assure that the 'imgData' and 'spatialData' are subsetted if columns/rows
# are dropped
#' @importFrom methods callNextMethod
#' @export
setMethod("[",
c("SpatialExperiment", "ANY", "ANY"),
function(x, i, j, ..., drop=FALSE) {
if (missing(i)) i <- TRUE
if (missing(j)) j <- TRUE
x <- callNextMethod()
if ( !isEmpty(imgData(x)) ) {
keep <- imgData(x)$sample_id %in% unique(x$sample_id)
imgData(x) <- imgData(x)[keep, ]
}
return(x)
}
)
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