Merge pull request #110 from hpages/devel

Compatibity with DelayedArray 0.31.7
MarioniLab · Jul 23, 2024 · ded6e8d · ded6e8d
2 parents ea70215 + 6e27ea9
commit ded6e8d
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Showing 4 changed files with 25 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DropletUtils
-Version: 1.25.0
-Date: 2022-11-21
+Version: 1.25.1
+Date: 2024-07-09
 Title: Utilities for Handling Single-Cell Droplet Data
 Authors@R: c(
     person("Aaron", "Lun", role = "aut"),
@@ -21,7 +21,8 @@ Imports:
     GenomicRanges,
     SummarizedExperiment,
     BiocParallel,
-    DelayedArray,
+    SparseArray (>= 1.5.18),
+    DelayedArray (>= 0.31.9),
     DelayedMatrixStats,
     HDF5Array,
     rhdf5,
@@ -63,4 +64,4 @@ LinkingTo:
     dqrng,
     scuttle
 SystemRequirements: C++11, GNU make
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -44,8 +44,10 @@ exportMethods(hashedDrops)
 exportMethods(removeAmbience)
 import(SingleCellExperiment)
 importClassesFrom(DelayedArray,DelayedArray)
-importClassesFrom(DelayedArray,SparseArraySeed)
+importClassesFrom(Matrix,CsparseMatrix)
 importClassesFrom(Matrix,dgCMatrix)
+importClassesFrom(SparseArray,COO_SparseArray)
+importClassesFrom(SparseArray,SparseArray)
 importFrom(BiocGenerics,match)
 importFrom(BiocParallel,SerialParam)
 importFrom(BiocParallel,bplapply)
@@ -54,15 +56,12 @@ importFrom(BiocParallel,bpnworkers)
 importFrom(BiocParallel,bpstart)
 importFrom(BiocParallel,bpstop)
 importFrom(DelayedArray,DelayedArray)
-importFrom(DelayedArray,SparseArraySeed)
 importFrom(DelayedArray,blockApply)
 importFrom(DelayedArray,colAutoGrid)
 importFrom(DelayedArray,currentViewport)
 importFrom(DelayedArray,getAutoBPPARAM)
 importFrom(DelayedArray,makeNindexFromArrayViewport)
-importFrom(DelayedArray,seed)
 importFrom(DelayedArray,setAutoBPPARAM)
-importFrom(DelayedArray,which)
 importFrom(DelayedArray,write_block)
 importFrom(DelayedMatrixStats,colMins)
 importFrom(DelayedMatrixStats,colQuantiles)

diff --git a/R/removeAmbience.R b/R/removeAmbience.R
@@ -109,7 +109,9 @@ NULL
 
 #' @importFrom methods is
 #' @importFrom stats pnbinom qnbinom
+#' @importClassesFrom Matrix CsparseMatrix
 #' @importFrom edgeR q2qnbinom
+#' @importClassesFrom SparseArray SparseArray
 #' @importFrom DelayedArray makeNindexFromArrayViewport write_block currentViewport
 .remap_quantiles <- function(block, matches, old.means, new.means, size.factors, group.sf, dispersion, sink) {
     vp <- currentViewport()
@@ -139,8 +141,10 @@ NULL
     if (!is.null(sink)) {
         write_block(sink, vp, q)
         NULL
-    } else if (is(block, "SparseArraySeed")) {
-        as(q, "CsparseMatrix")
+    } else if (is(block, "SparseArray")) {  # that's if we don't want to return
+        as(q, "CsparseMatrix")              # any SparseArray derivatives at
+                                            # all, even though SVT_SparseArray
+                                            # objects would probably be fine
     } else {
         q 
     }

diff --git a/R/utils.R b/R/utils.R
@@ -11,21 +11,19 @@
     as.integer(round(colSums(m)))
 }
 
-#' @importFrom DelayedArray DelayedArray SparseArraySeed which seed
-#' @importFrom beachmat whichNonZero
-#' @importClassesFrom DelayedArray DelayedArray SparseArraySeed
+#' @importClassesFrom SparseArray COO_SparseArray
+#' @importFrom DelayedArray setAutoBPPARAM DelayedArray
+#' @importClassesFrom DelayedArray DelayedArray
 .realize_DA_to_memory <- function(m, BPPARAM) {
     if (is(m, "DelayedArray")) {
-        if (!is(seed(m), "SparseArraySeed")) {
-            idx <- whichNonZero(m, BPPARAM)
-            m <- DelayedArray(
-                SparseArraySeed(
-                    nzindex=cbind(idx$i, idx$j), 
-                    nzdata=idx$x,
-                    dim=dim(m),
-                    dimnames=dimnames(m)
-                )
-            )
+        if (!is(m@seed, "COO_SparseArray")) {
+            # Coercion from DelayedArray to COO_SparseArray uses block
+            # processing.
+            old <- .parallelize(BPPARAM)
+            on.exit(setAutoBPPARAM(old))
+            new_seed <- as(m, "COO_SparseArray")
+
+            m <- DelayedArray(new_seed)
         }
     }