tidy up code and clean up namespace

DESCRIPTION

@@ -14,11 +14,12 @@ Imports:
     BiocSingular,
     BPCells (>= 0.1.0),
     cli,
-    DelayedArray,
+    DelayedArray (>= 0.28.0),
     Matrix,
     methods,
     rlang (>= 1.1.0),
-    S4Vectors
+    S4Vectors,
+    SparseArray
 Remotes: 
     bnprks/BPCells
 Suggests: 

NAMESPACE

@@ -103,6 +103,7 @@ exportMethods("^")
 exportMethods("dimnames<-")
 exportMethods(BPCellsSeed)
 exportMethods(DelayedArray)
+exportMethods(OLD_extract_sparse_array)
 exportMethods(acbind)
 exportMethods(arbind)
 exportMethods(binarize)
@@ -148,35 +149,39 @@ importClassesFrom(BiocSingular,BiocSingularParam)
 importClassesFrom(DelayedArray,DelayedArray)
 importClassesFrom(DelayedArray,DelayedMatrix)
 importClassesFrom(Matrix,dgCMatrix)
+importFrom(BiocSingular,runSVD)
 importFrom(DelayedArray,DelayedArray)
+importFrom(DelayedArray,OLD_extract_sparse_array)
+importFrom(DelayedArray,acbind)
+importFrom(DelayedArray,arbind)
+importFrom(DelayedArray,bindROWS)
+importFrom(DelayedArray,cbind)
+importFrom(DelayedArray,colVars)
+importFrom(DelayedArray,crossprod)
+importFrom(DelayedArray,extract_array)
+importFrom(DelayedArray,is_sparse)
+importFrom(DelayedArray,matrixClass)
 importFrom(DelayedArray,new_DelayedArray)
+importFrom(DelayedArray,path)
+importFrom(DelayedArray,rbind)
+importFrom(DelayedArray,rowVars)
+importFrom(DelayedArray,type)
+importFrom(S4Vectors,bindCOLS)
+importFrom(SparseArray,extract_sparse_array)
+importFrom(methods,cbind2)
+importFrom(methods,rbind2)
+importFrom(methods,show)
+importMethodsFrom(BPCells,"%*%")
 importMethodsFrom(BPCells,"[")
 importMethodsFrom(BPCells,"[<-")
 importMethodsFrom(BPCells,"^")
-importMethodsFrom(BiocSingular,runSVD)
-importMethodsFrom(DelayedArray,"%*%")
-importMethodsFrom(DelayedArray,"dimnames<-")
-importMethodsFrom(DelayedArray,DelayedArray)
-importMethodsFrom(DelayedArray,acbind)
-importMethodsFrom(DelayedArray,arbind)
-importMethodsFrom(DelayedArray,bindROWS)
-importMethodsFrom(DelayedArray,cbind)
-importMethodsFrom(DelayedArray,colMeans)
-importMethodsFrom(DelayedArray,colSums)
-importMethodsFrom(DelayedArray,colVars)
-importMethodsFrom(DelayedArray,crossprod)
+importMethodsFrom(BPCells,"dimnames<-")
+importMethodsFrom(BPCells,colMeans)
+importMethodsFrom(BPCells,colSums)
+importMethodsFrom(BPCells,rowMeans)
+importMethodsFrom(BPCells,rowSums)
+importMethodsFrom(BPCells,t)
+importMethodsFrom(DelayedArray,OLD_extract_sparse_array)
+importMethodsFrom(DelayedArray,dim)
 importMethodsFrom(DelayedArray,extract_array)
-importMethodsFrom(DelayedArray,extract_sparse_array)
 importMethodsFrom(DelayedArray,is_sparse)
-importMethodsFrom(DelayedArray,matrixClass)
-importMethodsFrom(DelayedArray,path)
-importMethodsFrom(DelayedArray,rbind)
-importMethodsFrom(DelayedArray,rowMeans)
-importMethodsFrom(DelayedArray,rowSums)
-importMethodsFrom(DelayedArray,rowVars)
-importMethodsFrom(DelayedArray,t)
-importMethodsFrom(DelayedArray,type)
-importMethodsFrom(S4Vectors,bindCOLS)
-importMethodsFrom(methods,cbind2)
-importMethodsFrom(methods,rbind2)
-importMethodsFrom(methods,show)

R/Class-BPCellsMatrix.R

@@ -27,7 +27,7 @@ methods::setClass("BPCellsMatrix",
 )
 
 #' @param x,object A `BPCellsMatrix` object.
-#' @importMethodsFrom methods show
+#' @importFrom methods show
 #' @export
 #' @rdname BPCellsMatrix-class
 methods::setMethod("show", "BPCellsMatrix", function(object) {
@@ -36,7 +36,7 @@ methods::setMethod("show", "BPCellsMatrix", function(object) {
 
 #' @return
 #' - `t`: A [BPCellsMatrix] object.
-#' @importMethodsFrom DelayedArray t
+#' @importMethodsFrom BPCells t
 #' @export
 #' @rdname BPCellsMatrix-class
 methods::setMethod("t", "BPCellsMatrix", function(x) {
@@ -132,9 +132,17 @@ methods::setClassUnion("ListOrNULL", c("list", "NULL"))
 
 # for `dim`, `dimnames`, `extract_array` and `is_sparse` just use the methods
 # from DelayedArray
+#' For BPCellsMatrix object
+#' @importMethodsFrom DelayedArray dim
+#' @importMethodsFrom DelayedArray extract_array
+#' @importMethodsFrom DelayedArray is_sparse
+#' @importMethodsFrom DelayedArray OLD_extract_sparse_array
+#' @noRd 
+NULL
+
 #' @return
 #' - `dimnames<-`: A [BPCellsRenameDimsMatrix][BPCellsRenameDims] object.
-#' @importMethodsFrom DelayedArray dimnames<-
+#' @importMethodsFrom BPCells dimnames<-
 #' @export
 #' @rdname BPCellsMatrix-class
 methods::setMethod(
@@ -149,21 +157,21 @@ methods::setMethod(
 #################### Matrix Statistics ########################
 #' BPCellsMatrix row/col summarization
 #'
-#' @importMethodsFrom DelayedArray rowSums
 #' @param x A [BPCellsMatrix][BPCellsMatrix-class] object.
 #' @return
 #' - `rowSums()`: vector of row sums
 #' @aliases rowSums
 #' @name BPCells-Summarization
 NULL
 
+#' @importMethodsFrom BPCells rowSums
 #' @export
 #' @rdname BPCells-Summarization
 methods::setMethod("rowSums", c(x = "BPCellsMatrix"), function(x) {
     rowSums(x@seed)
 })
 
-#' @importMethodsFrom DelayedArray colSums
+#' @importMethodsFrom BPCells colSums
 #' @return
 #' - `colSums()`: vector of col sums
 #' @aliases colSums
@@ -173,7 +181,7 @@ methods::setMethod("colSums", c(x = "BPCellsMatrix"), function(x) {
     colSums(x@seed)
 })
 
-#' @importMethodsFrom DelayedArray rowMeans
+#' @importMethodsFrom BPCells rowMeans
 #' @return
 #' - `rowMeans()`: vector of row means
 #' @aliases rowMeans
@@ -183,7 +191,7 @@ methods::setMethod("rowMeans", c(x = "BPCellsMatrix"), function(x) {
     rowMeans(x@seed)
 })
 
-#' @importMethodsFrom DelayedArray colMeans
+#' @importMethodsFrom BPCells colMeans
 #' @return
 #' - `colMeans()`: vector of col means
 #' @aliases colMeans
@@ -193,7 +201,7 @@ methods::setMethod("colMeans", c(x = "BPCellsMatrix"), function(x) {
     colMeans(x@seed)
 })
 
-#' @importMethodsFrom DelayedArray rowVars
+#' @importFrom DelayedArray rowVars
 #' @return
 #' - `rowVars()`: vector of row vars
 #' @aliases rowVars
@@ -206,7 +214,7 @@ methods::setMethod("rowVars", c(x = "BPCellsMatrix"), function(x) {
     stats$row_stats["variance", , drop = TRUE]
 })
 
-#' @importMethodsFrom DelayedArray colVars
+#' @importFrom DelayedArray colVars
 #' @return
 #' - `colVars()`: vector of col vars
 #' @aliases colVars

R/Class-BPCellsSeed.R

@@ -11,7 +11,7 @@
 #' @include utils.R
 methods::setClass("BPCellsSeed", contains = get_class("IterableMatrix"))
 
-#' @importMethodsFrom methods show
+#' @importFrom methods show
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod("show", "BPCellsSeed", function(object) {
@@ -22,7 +22,7 @@ methods::setMethod("show", "BPCellsSeed", function(object) {
 #' - `type`: A string. For all BPCells matrix type of `float` and `double`,
 #'   always return `double` since R cannot differentiate 32-bit and 64-bit real
 #'   number.
-#' @importMethodsFrom DelayedArray type
+#' @importFrom DelayedArray type
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod("type", "BPCellsSeed", function(x) {
@@ -35,15 +35,15 @@ methods::setMethod("type", "BPCellsSeed", function(x) {
 
 #' @return
 #' - `is_sparse`: Always return `TRUE` for `BPCellsSeed` object.
-#' @importMethodsFrom DelayedArray is_sparse
+#' @importFrom DelayedArray is_sparse
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod("is_sparse", "BPCellsSeed", function(x) TRUE)
 
 #' @inheritParams S4Arrays::extract_array
 #' @return
 #' - `extract_array`: A dense matrix.
-#' @importMethodsFrom DelayedArray extract_array
+#' @importFrom DelayedArray extract_array
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod(
@@ -56,18 +56,31 @@ methods::setMethod(
 )
 
 #' @return
-#' - `extract_sparse_array`: A [SparseArraySeed][DelayedArray::SparseArraySeed]
-#'   object.
-#' @importMethodsFrom DelayedArray extract_sparse_array
+#' - `OLD_extract_sparse_array`: A
+#'   [SparseArraySeed][DelayedArray::SparseArraySeed-class] object.
+#' @importFrom DelayedArray OLD_extract_sparse_array
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod(
-    "extract_sparse_array", "BPCellsSeed",
+    "OLD_extract_sparse_array", "BPCellsSeed",
     function(x, index) {
         methods::as(extract_bpcells_array(x, index), "SparseArraySeed")
     }
 )
 
+#' @return
+#' - `extract_sparse_array`: A
+#'   [SparseArray][SparseArray::SVT_SparseArray-class] object.
+#' @importFrom SparseArray extract_sparse_array
+#' @export
+#' @rdname BPCellsSeed-class
+methods::setMethod(
+    "extract_sparse_array", "BPCellsSeed",
+    function(x, index) {
+        methods::as(extract_bpcells_array(x, index), "SparseArray")
+    }
+)
+
 #######################################################################
 # All delayed operations should be wrapped into a `BPCellsSeed` object
 # In BPCells, `dimnames<-` was only defined for `IterableMatrix`.
@@ -80,6 +93,7 @@ methods::setMethod(
 #' @return
 #' - `dimnames<-`: A [BPCellsSeed] object, usually a `BPCellsRenameDimsSeed`
 #'   object.
+#' @importMethodsFrom BPCells dimnames<-
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod(
@@ -89,6 +103,7 @@ methods::setMethod(
     }
 )
 
+#' @importMethodsFrom BPCells dimnames<-
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod(
@@ -99,8 +114,9 @@ methods::setMethod(
 )
 
 # t will not change the underlying class
-#' @return - `t`: A [BPCellsSeed] object.
-#' @importMethodsFrom DelayedArray t
+#' @return
+#'  - `t`: A [BPCellsSeed] object.
+#' @importMethodsFrom BPCells t
 #' @export
 #' @rdname BPCellsSeed-class
 methods::setMethod("t", "BPCellsSeed", function(x) methods::callNextMethod())

R/Class-BindMatrix.R

@@ -68,7 +68,7 @@ methods::setClass("BPCellsColBindMatrixArray",
 #' @return
 #' - `DelayedArray`: A `BPCellsColBindMatrixMatrix` or
 #'   `BPCellsRowBindMatrixMatrix` object.
-#' @importMethodsFrom DelayedArray DelayedArray
+#' @importFrom DelayedArray DelayedArray
 #' @importFrom DelayedArray new_DelayedArray
 #' @export
 #' @rdname BPCellsBindMatrix
@@ -93,7 +93,7 @@ methods::setClass("BPCellsColBindMatrixMatrix",
     slots = c(seed = "BPCellsColBindMatrixSeed")
 )
 
-#' @importMethodsFrom DelayedArray matrixClass
+#' @importFrom DelayedArray matrixClass
 #' @export
 #' @rdname BPCellsBindMatrix
 methods::setMethod("matrixClass", "BPCellsColBindMatrixArray", function(x) {
@@ -145,7 +145,7 @@ methods::setClass("BPCellsRowBindMatrixArray",
     slots = c(seed = "BPCellsRowBindMatrixSeed")
 )
 
-#' @importMethodsFrom DelayedArray DelayedArray
+#' @importFrom DelayedArray DelayedArray
 #' @importFrom DelayedArray new_DelayedArray
 #' @export
 #' @rdname BPCellsBindMatrix
@@ -168,7 +168,7 @@ methods::setClass("BPCellsRowBindMatrixMatrix",
 )
 
 #' @export
-#' @importMethodsFrom DelayedArray matrixClass
+#' @importFrom DelayedArray matrixClass
 #' @rdname BPCellsBindMatrix
 methods::setMethod("matrixClass", "BPCellsRowBindMatrixArray", function(x) {
     "BPCellsRowBindMatrixMatrix"

R/Class-Convert.R

@@ -37,7 +37,7 @@ methods::setClass("BPCellsConvertArray",
 )
 
 #' @param seed A `BPCellsConvertSeed` object.
-#' @importMethodsFrom DelayedArray DelayedArray
+#' @importFrom DelayedArray DelayedArray
 #' @importFrom DelayedArray new_DelayedArray
 #' @export
 #' @rdname BPCellsConvert
@@ -59,7 +59,7 @@ methods::setClass("BPCellsConvertMatrix",
     slots = c(seed = "BPCellsConvertSeed")
 )
 
-#' @importMethodsFrom DelayedArray matrixClass
+#' @importFrom DelayedArray matrixClass
 #' @export
 #' @rdname BPCellsConvert
 methods::setMethod("matrixClass", "BPCellsConvertArray", function(x) {

R/Class-Dir.R

@@ -48,7 +48,7 @@ methods::setClass("BPCellsDirArray",
 )
 
 #' @param seed A `BPCellsDirSeed` object.
-#' @importMethodsFrom DelayedArray DelayedArray
+#' @importFrom DelayedArray DelayedArray
 #' @importFrom DelayedArray new_DelayedArray
 #' @export
 #' @rdname BPCellsDir
@@ -72,7 +72,7 @@ methods::setClass("BPCellsDirMatrix",
     slots = c(seed = "BPCellsDirSeed")
 )
 
-#' @importMethodsFrom DelayedArray matrixClass
+#' @importFrom DelayedArray matrixClass
 #' @export
 #' @rdname BPCellsDir
 methods::setMethod("matrixClass", "BPCellsDirArray", function(x) {

R/Class-Mask.R

@@ -37,7 +37,7 @@ methods::setClass("BPCellsMaskArray",
 )
 
 #' @param seed A `BPCellsMaskSeed` object.
-#' @importMethodsFrom DelayedArray DelayedArray
+#' @importFrom DelayedArray DelayedArray
 #' @importFrom DelayedArray new_DelayedArray
 #' @export
 #' @rdname BPCellsMask
@@ -60,7 +60,7 @@ methods::setClass("BPCellsMaskMatrix",
     slots = c(seed = "BPCellsMaskSeed")
 )
 
-#' @importMethodsFrom DelayedArray matrixClass
+#' @importFrom DelayedArray matrixClass
 #' @export
 #' @rdname BPCellsMask
 methods::setMethod("matrixClass", "BPCellsMaskArray", function(x) {

R/Class-Multiply.R

@@ -38,7 +38,7 @@ methods::setClass("BPCellsMultiplyArray",
 )
 
 #' @param seed A `BPCellsMultiplySeed` object.
-#' @importMethodsFrom DelayedArray DelayedArray
+#' @importFrom DelayedArray DelayedArray
 #' @importFrom DelayedArray new_DelayedArray
 #' @export
 #' @rdname BPCellsMultiply
@@ -60,7 +60,7 @@ methods::setClass("BPCellsMultiplyMatrix",
     slots = c(seed = "BPCellsMultiplySeed")
 )
 
-#' @importMethodsFrom DelayedArray matrixClass
+#' @importFrom DelayedArray matrixClass
 #' @export
 #' @rdname BPCellsMultiply
 methods::setMethod("matrixClass", "BPCellsMultiplyArray", function(x) {