@@ -2,9 +2,11 @@

 * Bioconductor 3.21, May 2025

-## zellkonverter 1.17.4

+## zellkonverter 1.17.4 (2025-04-10)

 * Add tests for **anndata** v0.10.9

+* Modify `SCE2AnnData()` to covert sparse matrices to `dgRMatrix` when they are

+  transposed (mostly assays) (Fixes #132)

 ## zellkonverter 1.17.3 (2025-04-08)

@@ -268,14 +268,18 @@ SCE2AnnData <- function(sce, X_name = NULL, assays = TRUE, colData = TRUE,

 #' @importClassesFrom Matrix CsparseMatrix

 #' @importFrom DelayedArray is_sparse

 #' @importFrom Matrix t

+# Original code from Charlotte Soneson in kevinrue/velociraptor

 .makeNumpyFriendly <- function(x, transpose = TRUE) {

     if (transpose) {

         x <- t(x)

     }

-    # Code from Charlotte Soneson in kevinrue/velociraptor.

     if (is_sparse(x)) {

-        as(x, "CsparseMatrix")

+        x <- as(x, "CsparseMatrix")

+        if (transpose) {

+            x <- as(x, "RsparseMatrix")

+        }

+        x

     } else {

         as.matrix(x)

     }

new file mode 100644

@@ -0,0 +1,38 @@

+test_that(".makeNumpyFriendly() works correctly", {

+    mat <- matrix(1:50, nrow = 10, ncol = 5)

+

+    friendly_mat <- .makeNumpyFriendly(mat, transpose = TRUE)

+    expect_identical(friendly_mat, t(mat))

+    expect_identical(dim(friendly_mat), rev(dim(mat)))

+

+    friendly_mat <- .makeNumpyFriendly(mat, transpose = FALSE)

+    expect_identical(friendly_mat, mat)

+    expect_identical(dim(friendly_mat), dim(mat))

+

+    sparse_mat <- Matrix::Matrix(mat, sparse = TRUE)

+    friendly_sparse_mat <- .makeNumpyFriendly(sparse_mat, transpose = TRUE)

+    expect_s4_class(friendly_sparse_mat, "dgRMatrix")

+    expect_identical(dim(friendly_sparse_mat), rev(dim(sparse_mat)))

+

+    friendly_sparse_mat <- .makeNumpyFriendly(sparse_mat, transpose = FALSE)

+    expect_s4_class(friendly_sparse_mat, "dgCMatrix")

+    expect_identical(dim(friendly_sparse_mat), dim(sparse_mat))

+

+    delayed_mat <- DelayedArray::DelayedArray(mat)

+    friendly_delayed_mat <- .makeNumpyFriendly(delayed_mat, transpose = TRUE)

+    expect_identical(friendly_delayed_mat, t(mat))

+    expect_identical(dim(friendly_delayed_mat), rev(dim(mat)))

+

+    friendly_delayed_mat <- .makeNumpyFriendly(delayed_mat, transpose = FALSE)

+    expect_identical(friendly_delayed_mat, mat)

+    expect_identical(dim(friendly_delayed_mat), dim(mat))

+

+    sparse_delayed_mat <- DelayedArray::DelayedArray(sparse_mat)

+    friendly_sparse_delayed_mat <- .makeNumpyFriendly(sparse_delayed_mat, transpose = TRUE)

+    expect_s4_class(friendly_sparse_delayed_mat, "dgRMatrix")

+    expect_identical(dim(friendly_sparse_delayed_mat), rev(dim(sparse_delayed_mat)))

+

+    friendly_sparse_delayed_mat <- .makeNumpyFriendly(sparse_delayed_mat, transpose = FALSE)

+    expect_s4_class(friendly_sparse_delayed_mat, "dgCMatrix")

+    expect_identical(dim(friendly_sparse_delayed_mat), dim(sparse_delayed_mat))

+})

@@ -35,6 +35,37 @@ test_that("writeH5AD works as expected", {

     expect_identical(col_data, colData(sce))

 })

+test_that("writeH5AD works as expected with version 0.10.9", {

+    temp <- tempfile(fileext = ".h5ad")

+    writeH5AD(sce, temp, version = "0.10.9")

+    expect_true(file.exists(temp))

+

+    # Reading it back out again. Hopefully we didn't lose anything important.

+    out <- readH5AD(temp, version = "0.10.9")

+

+    expect_identical(dimnames(out), dimnames(sce))

+    expect_equal(assay(out), assay(sce))

+    expect_identical(reducedDims(out), reducedDims(sce))

+

+    # Need to coerce the factors back to strings.

+    row_data <- rowData(out)

+    for (i in seq_len(ncol(row_data))) {

+        if (is.factor(row_data[[i]])) {

+            row_data[[i]] <- as.character(row_data[[i]])

+        }

+    }

+    expect_identical(row_data, rowData(sce))

+

+    col_data <- colData(out)

+    for (i in seq_len(ncol(col_data))) {

+        if (is.factor(col_data[[i]])) {

+            col_data[[i]] <- as.character(col_data[[i]])

+        }

+    }

+    names(col_data) <- names(colData(sce))

+    expect_identical(col_data, colData(sce))

+})

+

 test_that("writeH5AD works as expected with version 0.10.6", {

     temp <- tempfile(fileext = ".h5ad")

     writeH5AD(sce, temp, version = "0.10.6")