use prototyped S4Vectors::SimpleList as slots

Author: HelenaLC

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: spatialdataR
 Title: Representation of Python's spatialdata in R
 Depends: R (>= 4.6)
-Version: 0.99.38
+Version: 0.99.39
 Description: R interface to Python/scverse's 'spatialdata' framework for 
     unified spatial omics data handling. Adheres to OME-NGFF standards, 
     providing lazy, on-disk representations for multiscale images and 

NAMESPACE

@@ -42,6 +42,7 @@ exportMethods("instances<-")
 exportMethods("label<-")
 exportMethods("labelNames<-")
 exportMethods("labels<-")
+exportMethods("layer<-")
 exportMethods("point<-")
 exportMethods("pointNames<-")
 exportMethods("points<-")
@@ -133,6 +134,7 @@ importFrom(Rarr,read_zarr_attributes)
 importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,SimpleList)
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)

R/AllClasses.R

@@ -1,16 +1,81 @@
+#' @importFrom S4Vectors SimpleList
 #' @importFrom methods setClass setClassUnion setOldClass
 
+.sdLayerList <- setClass(
+    Class="sdLayerList", 
+    contains="SimpleList", 
+    slots=c(metadata="list"),
+    prototype=prototype(metadata=list()))
+
+.sdImageList <- setClass(
+    Class="sdImageList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataImage"))
+
+.sdLabelList <- setClass(
+    Class="sdLabelList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataLabel"))
+
+.sdPointList <- setClass(
+    Class="sdPointList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataPoint"))
+
+.sdShapeList <- setClass(
+    Class="sdShapeList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataShape"))
+
+.sdTableList <- setClass(
+    Class="sdTableList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SingleCellExperiment"))
+
+.sl <- S4Vectors:::new_SimpleList_from_list
+.ok <- \(x) length(x) == 1L && (is.list(x[[1L]]) || is(x[[1L]], "SimpleList"))
+
+sdImageList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdImageList", as.list(x))
+}
+
+sdLabelList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdLabelList", as.list(x))
+}
+
+sdPointList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdPointList", as.list(x))
+}
+
+sdShapeList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdShapeList", as.list(x))
+}
+
+sdTableList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdTableList", as.list(x))
+}
+
 #' @export
 #' @rdname SpatialData
 .SpatialData <- setClass(
     Class="SpatialData",
     contains=c("list", "Annotated"),
     representation(
-        images="list",  # 'SpatialDataImage's
-        labels="list",  # 'SpatialDataLabel's
-        points="list",  # 'SpatialDataPoint's
-        shapes="list",  # 'SpatialDataShape's
-        tables="list")) # 'SingleCellExperiment's
+        images="sdImageList",
+        labels="sdLabelList",
+        points="sdPointList",
+        shapes="sdShapeList",
+        tables="sdTableList")) 
 
 .LAYERS <- `names<-`(. <- c("images","labels","points","shapes","tables"), .)
 .SpatialDataAttrs <- setClass("SpatialDataAttrs", contains="list")

R/AllGenerics.R

@@ -84,6 +84,7 @@ setGeneric("meta<-", \(x, ..., value) standardGeneric("meta<-"))
 setGeneric("data<-", \(x, ..., value) standardGeneric("data<-"))
 
 setGeneric("layer", \(x, i, ...) standardGeneric("layer"))
+setGeneric("layer<-", \(x, i, value) standardGeneric("layer<-"))
 setGeneric("element", \(x, i, ...) standardGeneric("element"))
 setGeneric("element<-", \(x, i, value) standardGeneric("element<-"))
 setGeneric("elements", \(x, i, ...) standardGeneric("elements"))

R/SpatialData.R

@@ -53,13 +53,17 @@
 #' x[c(1, 2), list(1, c(1, 2))] # multiple
 #' 
 #' @export
-SpatialData <- \(images, labels, points, shapes, tables) {
-    if (missing(images)) images <- list()
-    if (missing(labels)) labels <- list()
-    if (missing(points)) points <- list()
-    if (missing(shapes)) shapes <- list()
-    if (missing(tables)) tables <- list()
+SpatialData <- \(
+    images=list(), 
+    labels=list(), 
+    points=list(), 
+    shapes=list(), 
+    tables=list())
+{
     .SpatialData(
-        images=images, labels=labels, 
-        points=points, shapes=shapes, tables=tables)
+        images=sdImageList(images),
+        labels=sdLabelList(labels),
+        points=sdPointList(points),
+        shapes=sdShapeList(shapes),
+        tables=sdTableList(tables))
 }