avoid (some) namespace conflicts

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
 Depends: R (>= 4.6)
-Version: 0.99.36
+Version: 0.99.37
 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

@@ -113,7 +113,6 @@ exportMethods(tables)
 exportMethods(transform)
 exportMethods(translation)
 import(geoarrow)
-importClassesFrom(S4Vectors,DFrame)
 importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,combine)
@@ -136,6 +135,7 @@ importFrom(S4Vectors,isSequence)
 importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,setValidity2)
+importFrom(S4Vectors,transform)
 importFrom(SingleCellExperiment,"int_colData<-")
 importFrom(SingleCellExperiment,"int_metadata<-")
 importFrom(SingleCellExperiment,SingleCellExperiment)
@@ -188,8 +188,10 @@ importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,is)
 importFrom(methods,new)
+importFrom(methods,setClass)
 importFrom(methods,setClassUnion)
 importFrom(methods,setMethod)
+importFrom(methods,setOldClass)
 importFrom(methods,setReplaceMethod)
 importFrom(rlang,"!!")
 importFrom(rlang,.data)

R/AllClasses.R

@@ -1,53 +1,7 @@
-.SpatialDataAttrs <- setClass(
-    Class="SpatialDataAttrs",
-    contains="list")
+#' @importFrom methods setClass setClassUnion setOldClass
 
-.SpatialDataImage <- setClass(
-    Class="SpatialDataImage",
-    contains=c("Annotated"),
-    slots=list(data="list", meta="SpatialDataAttrs"))
-
-.SpatialDataLabel <- setClass(
-    Class="SpatialDataLabel",
-    contains=c("Annotated"),
-    slots=list(data="list", meta="SpatialDataAttrs"))
-
-# these are 'R6ClassGenerator's;
-# this somehow does the trick...
-setClass("FileSystemDataset", "VIRTUAL")
-setClass("arrow_dplyr_query", "VIRTUAL")
-setClass("tbl_duckdb_connection", "VIRTUAL")
-setClass("duckspatial_df", "VIRTUAL")
-setClass("Table", "VIRTUAL")
-
-# TODO: this isn't great... arrow::open_dataset gives a FileSystemDataset,
-# read_parquet gives a Table, dplyr calls give a query, but also wanna
-# be able to store a normal data.frame, maybe?
-#' @importFrom methods setClassUnion
-setClassUnion(
-    "arrow_OR_df",
-    c("tbl_duckdb_connection", "duckspatial_df", "FileSystemDataset", "Table", "arrow_dplyr_query", "data.frame"))
-
-.SpatialDataPoint <- setClass(
-    Class="SpatialDataPoint",
-    contains=c("Annotated"),
-    slots=list(data="arrow_OR_df", meta="SpatialDataAttrs"))
-
-#' @importClassesFrom S4Vectors DFrame
-.SpatialDataShape <- setClass(
-    Class="SpatialDataShape",
-    contains=c("Annotated"),
-    slots=list(data="arrow_OR_df", meta="SpatialDataAttrs"))
-
-setClassUnion("SpatialDataArray", c("SpatialDataImage", "SpatialDataLabel"))
-setClassUnion("SpatialDataFrame", c("SpatialDataPoint", "SpatialDataShape"))
-
-setClassUnion("SpatialDataElement", c(
-    "SpatialDataImage", "SpatialDataLabel", 
-    "SpatialDataPoint", "SpatialDataShape"))
-
-#' @rdname SpatialData
 #' @export
+#' @rdname SpatialData
 .SpatialData <- setClass(
     Class="SpatialData",
     contains=c("list", "Annotated"),
@@ -58,5 +12,24 @@ setClassUnion("SpatialDataElement", c(
         shapes="list",  # 'SpatialDataShape's
         tables="list")) # 'SingleCellExperiment's
 
-. <- c("images", "labels", "points", "shapes", "tables")
-names(.LAYERS) <- .LAYERS <- .
+.LAYERS <- `names<-`(. <- c("images","labels","points","shapes","tables"), .)
+.SpatialDataAttrs <- setClass("SpatialDataAttrs", contains="list")
+setOldClass("duckspatial_df")
+
+setClass("SpatialDataArray", 
+    contains=c("Annotated", "VIRTUAL"),
+    slots=list(data="list", meta="SpatialDataAttrs"))
+
+setClass("SpatialDataFrame",
+    contains=c("Annotated", "VIRTUAL"),
+    slots=list(data="duckspatial_df", meta="SpatialDataAttrs"))
+
+.SpatialDataImage <- setClass("SpatialDataImage", contains="SpatialDataArray")
+.SpatialDataLabel <- setClass("SpatialDataLabel", contains="SpatialDataArray")
+
+.SpatialDataPoint <- setClass("SpatialDataPoint", contains="SpatialDataFrame")
+.SpatialDataShape <- setClass("SpatialDataShape", contains="SpatialDataFrame")
+
+setClassUnion("SpatialDataElement", c(
+    "SpatialDataImage", "SpatialDataLabel", 
+    "SpatialDataPoint", "SpatialDataShape"))

R/AllGenerics.R

@@ -4,13 +4,11 @@ setGeneric("image", \(x, ...) standardGeneric("image"))
 setGeneric("label", \(x, ...) standardGeneric("label"))
 setGeneric("shape", \(x, ...) standardGeneric("shape"))
 setGeneric("point", \(x, ...) standardGeneric("point"))
-#setGeneric("table", \(x, ...) standardGeneric("table"))
-#' @importFrom BiocGenerics table
 
 # get all ----
 
 setGeneric("images", \(x, ...) standardGeneric("images"))
-setGeneric("labels", \(x, ...) standardGeneric("labels"))
+setGeneric("labels", \(object, ...) standardGeneric("labels"))
 setGeneric("shapes", \(x, ...) standardGeneric("shapes"))
 setGeneric("points", \(x, ...) standardGeneric("points"))
 setGeneric("tables", \(x, ...) standardGeneric("tables"))
@@ -63,7 +61,6 @@ setGeneric("addCT", \(x, ...) standardGeneric("addCT"))
 setGeneric("scale", \(x, t, ...) standardGeneric("scale"))
 setGeneric("rotate", \(x, t, ...) standardGeneric("rotate"))
 setGeneric("sequence", \(x, t, ...) standardGeneric("sequence"))
-setGeneric("transform", \(x, i, ...) standardGeneric("transform"))
 setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
 
 setGeneric("flip", \(x, ...) standardGeneric("flip"))

R/SpatialData.R

@@ -26,7 +26,7 @@
 #' @param points list of \code{\link{SpatialDataPoint}}s
 #' @param shapes list of \code{\link{SpatialDataShape}}s
 #' @param tables list of \code{SingleCellExperiment}s
-#' @param x \code{SpatialData}
+#' @param x,object \code{SpatialData} object.
 #' @param i,j character string, scalar or vector of indices
 #'   specifying the element to extract from a given layer.
 #' @param drop ignored.

R/mask.R

@@ -69,7 +69,7 @@ setMethod("mask", c("SpatialData", "ANY", "ANY"), \(x, i, j, k,
     .i <- transform(.i, ct[k])
     .j <- transform(.j, ct[k])
     t <- tryCatch(error=\(.) NULL, getTable(x, i))
-    se <- .mask(.i, .j, how=how, table=t, ...)
+    se <- mask_i_by_j(.i, .j, how=how, table=t, ...)
     ik <- if (is.null(t)) "instance" else instance_key(t)
     md <- list(region=j, region_key="region", instance_key=ik)
     int_metadata(se)$spatialdata_attrs <- md
@@ -81,14 +81,18 @@ setMethod("mask", c("SpatialData", "ANY", "ANY"), \(x, i, j, k,
     `table<-`(x, nm, value=se)
 })
 
-setGeneric(".mask", \(i, j, ...) standardGeneric(".mask"))
+# internal use only!
+#' @noRd
+setGeneric("mask_i_by_j", \(i, j, ...) standardGeneric("mask_i_by_j"))
 
 #' @noRd
 #' @importFrom methods as
 #' @importFrom Matrix sparseVector
 #' @importFrom SummarizedExperiment assayNames<-
 #' @importFrom SingleCellExperiment SingleCellExperiment
-setMethod(".mask", c("SpatialDataImage", "SpatialDataLabel"), \(i, j, how=NULL, ...) {
+setMethod("mask_i_by_j", 
+    c("SpatialDataImage", "SpatialDataLabel"), 
+    \(i, j, how=NULL, ...) {
     .wh <- \(.) {
         ds <- dim(.); if (length(ds) == 3) ds <- ds[-1]
         metadata(.)$wh %||% list(c(0, ds[2]), c(0, ds[1]))
@@ -129,7 +133,9 @@ setMethod(".mask", c("SpatialDataImage", "SpatialDataLabel"), \(i, j, how=NULL,
 #' @importFrom SparseArray colSums
 #' @importFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom dplyr mutate left_join coalesce join_by select count collect row_number
-setMethod(".mask", c("SpatialDataPoint", "SpatialDataShape"), \(i, j, how=NULL, ...) {
+setMethod("mask_i_by_j", 
+    c("SpatialDataPoint", "SpatialDataShape"), 
+    \(i, j, how=NULL, ...) {
     if (!is.null(how)) message("Can only count when masking points; ignoring 'how'")
     id_x <- id_y <- n <- NULL # R CMD check
     ij <- .mask_map(i, j)
@@ -162,7 +168,9 @@ setMethod(".mask", c("SpatialDataPoint", "SpatialDataShape"), \(i, j, how=NULL,
 #' @importFrom SummarizedExperiment assay
 #' @importFrom duckspatial ddbs_intersects
 #' @importFrom SingleCellExperiment SingleCellExperiment
-setMethod(".mask", c("SpatialDataShape", "SpatialDataShape"), \(i, j, how=NULL, table=NULL, assay=1, ...) {
+setMethod("mask_i_by_j", 
+    c("SpatialDataShape", "SpatialDataShape"), 
+    \(i, j, how=NULL, table=NULL, assay=1, ...) {
     # validity
     if (is.null(table)) stop("Missing 'table'; can't mask shapes without")
     if (is.null(how)) { how <- "sum"; message("Missing 'how'; defaulting to 'sum'") }
@@ -201,5 +209,5 @@ setMethod(".mask", c("SpatialDataShape", "SpatialDataShape"), \(i, j, how=NULL,
 })
 
 #' @noRd
-setMethod(".mask", c("ANY", "ANY"), \(i, j, ...)
+setMethod("mask_i_by_j", c("ANY", "ANY"), \(i, j, ...)
     stop("'mask'ing between these element types not supported"))

R/methods.R

@@ -90,16 +90,16 @@ setReplaceMethod("meta", c("SpatialDataElement", "list"),
     names(j) <- rownames(x)[ne > 0]
     for (. in names(j)) {
         .j <- j[[.]]
-        n <- length(attr(x, .))
+        n <- length(x[[.]])
         if (is.character(.j)) {
-            if (!all(.j %in% names(attr(x, .))))
+            if (!all(.j %in% names(x[[.]])))
                 stop("invalid 'j'")
         } else if (length(.j) == 1 && is.infinite(.j)) {
             .j <- n
         } else if (any(.j > n)) {
             stop("invalid 'j'")
         }
-        attr(x, .) <- attr(x, .)[.j]
+        x[[.]] <- x[[.]][.j]
     }
     x
 }
@@ -133,17 +133,20 @@ setMethod("colnames", "SpatialData", \(x) {
 
 # layer ----
 
+.invalid_i <- paste(
+    "invalid 'i'; should be a string or scalar integer",
+    "specifying the name or position of an element in 'x'")
+
 #' @rdname SpatialData
 #' @export
 setMethod("layer", c("SpatialData", "character"), \(x, i) {
-    stopifnot(i %in% unlist(colnames(x)), length(i) == 1)
+    match.arg(i, unlist(colnames(x)))
     names(Filter(\(.) i %in% ., colnames(x)))
 })
 
 #' @rdname SpatialData
 #' @export
-setMethod("layer", c("SpatialData", "ANY"), \(x, i) 
-    stop("invalid 'i'; should be a string specifying an element in 'x'"))
+setMethod("layer", c("SpatialData", "ANY"), \(x, i) stop(.invalid_i))
 
 # element ----
 
@@ -163,8 +166,7 @@ setMethod("element", c("SpatialData", "missing"), \(x, i) element(x, 1))
 
 #' @rdname SpatialData
 #' @export
-setMethod("element", c("SpatialData", "ANY"), \(x, i) 
-    stop("invalid 'i'; should be a string specifying an element in 'x'"))
+setMethod("element", c("SpatialData", "ANY"), \(x, i) stop(.invalid_i))
 
 #' @rdname SpatialData
 #' @export
@@ -180,7 +182,7 @@ setMethod("images", "SpatialData", \(x) x$images)
 
 #' @export
 #' @rdname SpatialData
-setMethod("labels", "SpatialData", \(x) x$labels)
+setMethod("labels", "SpatialData", \(object) object$labels)
 
 #' @export
 #' @rdname SpatialData
@@ -196,8 +198,7 @@ setMethod("tables", "SpatialData", \(x) x$tables)
 
 # get nms ----
 
-one <- c("image", "label", "point", "shape", "table")
-all <- paste0(one, "s")
+all <- paste0(one <- c("image", "label", "point", "shape", "table"), "s")
 
 #' @name SpatialData
 #' @exportMethod imageNames labelNames pointNames shapeNames tableNames
@@ -248,16 +249,17 @@ NULL
     y[[i]]
 }
 
-#' @name SpatialData
 #' @export
+#' @name SpatialData
+#' @importFrom BiocGenerics table
 setMethod("table", "ANY", \(...) {
     l <- list(...)
-    if (!is(l[[1]], "SpatialData")) 
+    if (!is(l[[1]], "SpatialData"))
         return(base::table(...))
     n <- length(l)
     i <- if (n == 1) 1 else l[[2]]
     m <- length(i)
-    if (any(c(n, m) > 2)) 
+    if (n > 2 || m > 1)
         stop("too many arguments")
     y <- l[[1]]$tables
     .get(y, i)
@@ -321,17 +323,17 @@ for (. in all) eval(f(.), parent.env(environment()))
 
 # set one ----
 
+#' @name SpatialData
+#' @exportMethod image<- label<- point<- shape<- table<-
+NULL
+
 typ <- c(
     image="SpatialDataImage", 
     label="SpatialDataLabel", 
     point="SpatialDataPoint", 
     shape="SpatialDataShape", 
     table="SingleCellExperiment")
 
-#' @name SpatialData
-#' @exportMethod image<- label<- point<- shape<- table<-
-NULL
-
 f <- \(.) setReplaceMethod(., 
     c("SpatialData", "character", typ[[.]]), 
     \(x, i, value) {

R/read.R

@@ -87,19 +87,6 @@ readPoint <- function(x, ...) {
     SpatialDataPoint(data=df, meta=SpatialDataAttrs(md))
 }
 
-# create DuckDB connection
-# (to be used everywhere!)
-#' @importFrom DBI dbIsValid
-#' @importFrom duckspatial ddbs_create_conn
-.conn <- \() {
-    nm <- ".SpatialData_DuckDB_conn"
-    if (!exists(nm, envir=.GlobalEnv) ||
-        !dbIsValid(.GlobalEnv[[nm]])) {
-        .GlobalEnv[[nm]] <- ddbs_create_conn()
-    }
-    .GlobalEnv[[nm]]
-}
-
 #' @rdname readSpatialData
 #' @importFrom Rarr read_zarr_attributes
 #' @importFrom duckspatial ddbs_open_dataset