use BiocGenerics::data

Author: HelenaLC

NAMESPACE

@@ -115,6 +115,7 @@ exportMethods(translation)
 importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,combine)
+importFrom(BiocGenerics,data)
 importFrom(BiocGenerics,rownames)
 importFrom(BiocGenerics,table)
 importFrom(BiocGenerics,transform)

R/AllGenerics.R

@@ -83,11 +83,9 @@ setGeneric("instance_key<-", \(x, value) standardGeneric("instance_key<-"))
 
 # uts ----
 
-setGeneric("data", \(...) standardGeneric("data"))
 setGeneric("meta", \(x, ...) standardGeneric("meta"))
-
-setGeneric("data<-", \(x, ..., value) standardGeneric("data<-"))
 setGeneric("meta<-", \(x, ..., value) standardGeneric("meta<-"))
+setGeneric("data<-", \(x, ..., value) standardGeneric("data<-"))
 
 setGeneric("layer", \(x, i, ...) standardGeneric("layer"))
 setGeneric("element", \(x, i, ...) standardGeneric("element"))

R/methods.R

@@ -27,15 +27,10 @@ setMethod("[[", c("SpatialData", "character"), \(x, i, ...) attr(x, i))
 
 #' @export
 #' @rdname SpatialData
-setMethod("data", "ANY", \(...) {
-    l <- list(...)
-    x <- l[[1]]
-    if (!is(x, "SpatialDataElement")) 
-        return(utils::data(...))
-    if (!is(x, "SpatialDataArray")) 
-        return(x@data)
+#' @importFrom BiocGenerics data
+setMethod("data", "SpatialDataElement", \(x, k=1, ...) {
+    if (!is(x, "SpatialDataArray")) return(x@data)
     # return list of available scales
-    k <- if (length(l) == 1) 1 else l[[2]]
     if (is.null(k)) return(x@data)
     # should be a scalar positive integer
     ok <- length(k) == 1 && is.numeric(k) && k > 0 && k == round(k)