add altexp handling

R/make-seurat.R

@@ -75,6 +75,10 @@ sce_to_seurat <- function(
       return(mat)
     })
 
+  # pull out any altExps to handle manually
+  alt_exps <- altExps(sce)
+  altExps(sce) <- NULL
+
   # Let Seurat do initial conversion to capture most things
   sobj <- Seurat::as.Seurat(sce)
 
@@ -107,6 +111,18 @@ sce_to_seurat <- function(
     sobj[["spliced"]] <- create_seurat_assay(counts = assay(sce, "spliced"))
   }
 
+  # add altExps as needed.
+  for (alt_exp_name in names(alt_exps)) {
+    alt_exp <- alt_exps[[alt_exp_name]]
+    stopifnot(
+      "All altExps must contain a `counts` assay." = "counts" %in% assayNames(alt_exp)
+    )
+    sobj[[alt_exp_name]] <- create_seurat_assay(counts = counts(alt_exp))
+    if ("logcounts" %in% assayNames(alt_exp)) {
+      sobj[[alt_exp_name]]$data <- logcounts(alt_exp)
+    }
+  }
+
   # add sample-level metadata after removing non-vector objects
   sobj@misc <- sce_meta |>
     purrr::discard(is.object) |>

tests/testthat/test-make-seurat.R

@@ -120,3 +120,21 @@ test_that("SCE to Seurat with id conversion and 10x reference works as expected"
     dim(reducedDim(sce, "UMAP"))
   )
 })
+
+test_that("conversion works with altExps", {
+  sce <- readRDS(test_path("data", "scpca_sce.rds"))
+  altsce <- SingleCellExperiment(assays = list(counts = counts(sce), logcounts = logcounts(sce)))
+  altExps(sce) <- list(
+    alt1 = altsce,
+    alt2 = altsce
+  )
+
+  seurat_obj <- sce_to_seurat(sce, use_symbols = FALSE)
+
+  expect_equal(dim(seurat_obj), dim(sce))
+  expect_setequal(rownames(seurat_obj), rownames(sce))
+  expect_setequal(colnames(seurat_obj), colnames(sce))
+
+  expect_setequal(names(seurat_obj@assays), c("RNA", "spliced", "alt1", "alt2"))
+  expect_equal(Seurat::DefaultAssay(seurat_obj), "RNA")
+})