Add support for assays stored as SeuratObject::Assay5 (#23)

DESCRIPTION

@@ -14,7 +14,8 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
     testthat (>= 3.0.0),
-    Matrix
+    Matrix,
+    SeuratObject (>= 5.0.0)
 Config/testthat/edition: 3
 Imports:
     methods,

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(counts_matrix_from_assay)
 export(create_bugreport)
 export(create_bugreport_from_seurat)
 export(create_loupe)

R/err.R

@@ -60,9 +60,10 @@ create_bugreport_from_seurat <- function(obj) {
   assay <- namedAssay[[1]]
   clusters <- select_clusters(obj)
   projections <- select_projections(obj)
+  counts <- counts_matrix_from_assay(assay)
 
   create_bugreport(
-    assay@counts,
+    counts,
     clusters,
     projections,
     assay_name = assay_name,

R/lib.R

@@ -44,6 +44,7 @@ create_loupe_from_seurat <- function(
 
   assay_name <- names(namedAssay)
   assay <- namedAssay[[1]]
+  counts <- counts_matrix_from_assay(assay)
 
   clusters <- select_clusters(obj, dedup=dedup_clusters)
   projections <- select_projections(obj)
@@ -58,7 +59,7 @@ create_loupe_from_seurat <- function(
   }
 
   success <- create_loupe(
-    assay@counts,
+    counts,
     clusters=clusters,
     projections=projections,
     output_dir=output_dir,

R/util.R

@@ -56,8 +56,9 @@ select_assay <- function(obj) {
   for (i in seq_along(assay_priority)) {
     name <- names(assay_priority[i])
     assay <- Seurat::GetAssay(obj, assay=name)
+    counts <- counts_matrix_from_assay(assay)
 
-    if (length(assay@counts) > 0) {
+    if (length(counts) > 0) {
       result = list()
       result[[name]] = assay
       return(result)
@@ -67,6 +68,25 @@ select_assay <- function(obj) {
   NULL
 }
 
+#' Extract the counts matrix from the Assay
+#'
+#' @param assay A SeuratObject::Assay or SeuratObject::Assay5
+#'
+#' @return A sparse counts matrix
+#'
+#' @export
+counts_matrix_from_assay <- function(assay) {
+  if (packageVersion("Seurat") >= 5) {
+    return(assay$counts)
+  } else {
+    if (is(assay, 'Assay5')) {
+      stop("Cannot get count matrix: Please upgrade to Seurat > 5 to support dataset")
+    }
+
+    return(assay@counts)
+  }
+}
+
 #' Select clusters from the assay
 #'
 #' @param obj A Seurat Object

README.md

@@ -37,9 +37,12 @@ library("loupeR")
 # Gene Expression RNA assay
 assay <- seurat_obj[["RNA"]]
 
+# get counts matrix from either the old or newer formats of assay
+counts <- counts_matrix_from_assay(assay)
+
 # convert the count matrix, clusters, and projections into a Loupe file
 create_loupe(
-    assay@counts,
+    counts,
     clusters = select_clusters(seurat_obj),
     projections = select_projections(seurat_obj)
 )

tests/testthat/test-util.R

@@ -4,15 +4,29 @@ test_that("select_assay selects active assay", {
   rna3 <- create_count_mat(5, 5)
 
   obj <- Seurat::CreateSeuratObject(rna1, assay="rna1")
-  obj[["rna2_"]] = Seurat::CreateAssayObject(rna2, key="rna2_")
-  obj[["rna3_"]] = Seurat::CreateAssayObject(rna3, key="rna3_")
+  obj[["rna2"]] = Seurat::CreateAssayObject(rna2, key="rna2_")
+  obj[["rna3"]] = Seurat::CreateAssayObject(rna3, key="rna3_")
 
   expect_equal(Seurat::DefaultAssay(object = obj), "rna1")
-  Seurat::DefaultAssay(object = obj) <- "rna2_"
-  expect_equal(Seurat::DefaultAssay(object = obj), "rna2_")
+  Seurat::DefaultAssay(object = obj) <- "rna2"
+  expect_equal(Seurat::DefaultAssay(object = obj), "rna2")
 
   assay <- select_assay(obj)
-  expect_equal(names(assay), "rna2_")
+  expect_equal(names(assay), "rna2")
+})
+
+test_that("counts_matrix_from_assay works on different assay version", {
+  rna1 <- create_count_mat(5, 5)
+  rna2 <- create_count_mat(5, 5)
+  rna3 <- create_count_mat(5, 5)
+
+  obj <- Seurat::CreateSeuratObject(rna1, assay="rna1")
+  obj[["rna2"]] = Seurat::CreateAssayObject(rna2, key="rna2_")
+  obj[["rna3"]] = SeuratObject::CreateAssay5Object(rna3, key="rna3_")
+
+  expect_equal(counts_matrix_from_assay(obj[["rna1"]]), rna1)
+  expect_equal(counts_matrix_from_assay(obj[["rna2"]]), rna2)
+  expect_equal(counts_matrix_from_assay(obj[["rna3"]]), rna3)
 })
 
 test_that("select_clusters selects Idents", {