[r] Make SOMAs and X layers selectable when converting to a Seurat object

apis/python/examples/soco-batch-query.py

@@ -33,7 +33,7 @@
 for i, ctot_id in enumerate(ctot_ids):
     soma_slices = soco.query(
         obs_attrs=["cell_type_ontology_term_id"],
-        obs_query_string=f'cell_type_ontology_term_id == "{ctot_id}"',
+        obs_query_string=f'cell_type_ontology_term_id == {ctot_id!r}',
     )
     if soma_slices == []:
         continue

apis/python/examples/uniformizer.py

@@ -67,7 +67,7 @@ def main() -> int:
         return uniformizer.add_soma(args.dataset_id, args.soma)
     else:
         raise Exception(
-            f'Internal coding error: handler for "{args.func_name}" not found.'
+            f'Internal coding error: handler for {args.func_name!r} not found.'
         )
 
 

apis/python/src/tiledbsoma/annotation_dataframe.py

@@ -94,7 +94,7 @@ def __repr__(self) -> str:
         """
         Default display of soma.obs and soma.var.
         """
-        return ", ".join(f"'{key}'" for key in self.keys())
+        return ", ".join(f"{key!r}" for key in self.keys())
 
     # ----------------------------------------------------------------
     def __len__(self) -> int:

apis/python/src/tiledbsoma/annotation_matrix_group.py

@@ -47,7 +47,7 @@ def __repr__(self) -> str:
         """
         Default display of soma.obsm and soma.varm.
         """
-        return ", ".join(f"'{key}'" for key in self.keys())
+        return ", ".join(f"{key!r}" for key in self.keys())
 
     # ----------------------------------------------------------------
     def __iter__(self) -> Iterator[AnnotationMatrix]:
@@ -68,7 +68,7 @@ def __getattr__(self, name: str) -> Optional[AnnotationMatrix]:
         with self._open() as G:
             if name not in G:
                 raise AttributeError(
-                    f"'{self.__class__.__name__}' object has no attribute '{name}'"
+                    f"{self.__class__.__name__!r} object has no attribute {name!r}"
                 )
         return self[name]
 

apis/python/src/tiledbsoma/annotation_pairwise_matrix_group.py

@@ -57,7 +57,7 @@ def __repr__(self) -> str:
         """
         Default display of soma.obsp and soma.varp.
         """
-        return ", ".join(f"'{key}'" for key in self.keys())
+        return ", ".join(f"{key!r}" for key in self.keys())
 
     # ----------------------------------------------------------------
     def __getattr__(self, name: str) -> Optional[AssayMatrix]:
@@ -68,7 +68,7 @@ def __getattr__(self, name: str) -> Optional[AssayMatrix]:
         with self._open() as G:
             if name not in G:
                 raise AttributeError(
-                    f"'{self.__class__.__name__}' object has no attribute '{name}'"
+                    f"{self.__class__.__name__!r} object has no attribute {name!r}"
                 )
         return self[name]
 

apis/python/src/tiledbsoma/assay_matrix_group.py

@@ -54,7 +54,7 @@ def __repr__(self) -> str:
         """
         Default display of soma.X.
         """
-        return ", ".join(f"'{key}'" for key in self.keys())
+        return ", ".join(f"{key!r}" for key in self.keys())
 
     # ----------------------------------------------------------------
     def __getattr__(self, name: str) -> Optional[AssayMatrix]:
@@ -65,7 +65,7 @@ def __getattr__(self, name: str) -> Optional[AssayMatrix]:
         with self._open() as G:
             if name not in G:
                 raise AttributeError(
-                    f"'{self.__class__.__name__}' object has no attribute '{name}'"
+                    f"{self.__class__.__name__!r} object has no attribute {name!r}"
                 )
         return self[name]
 

apis/python/src/tiledbsoma/util_tiledb.py

@@ -89,7 +89,7 @@ def show_tiledb_group_array_schemas(uri: str, ctx: Optional[tiledb.Ctx] = None)
 
 # ----------------------------------------------------------------
 def list_fragments(array_uri: str) -> None:
-    print(f"Listing fragments for array: '{array_uri}'")
+    print(f"Listing fragments for array: {array_uri!r}")
     vfs = tiledb.VFS()
 
     fragments = []

apis/r/DESCRIPTION

@@ -7,7 +7,7 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices,
     from and export to in-memory formats used by popular toolchains like
     'Seurat', 'Bioconductor', and even 'AnnData' using the companion Python
     package.
-Version: 0.1.22.9000
+Version: 0.1.22.9001
 Authors@R: c(
     person(given = "Aaron",
            family = "Wolen",

apis/r/NEWS.md

@@ -2,7 +2,8 @@
 
 ## Features
 
-* New function `dataset_seurat_pbmc3k()` to download the pbmc3k dataset from 10X and import as a `Seurat` object without requiring any extra dependencies.
+- The `SOMACollection`'s `to_seurat()` method gains a `somas` argument that makes it possible to select a subset of `SOMA`s and `X` layers to be retrieved (#571).
+- New function `dataset_seurat_pbmc3k()` to download the pbmc3k dataset from 10X and import as a `Seurat` object without requiring any extra dependencies.
 
 # tiledbsoma 0.1.19
 
@@ -14,15 +15,15 @@
 
 ## Features
 
-- The `AnnotationMatrix`'s `to_matrix()` method now supports batched reads via the `batch_mode` argument. This functionality can also be leveraged from `SOMA`'s  `get_seurat_dimreductions_list()` and `get_seurat_dimreduction()` methods.
+- The `AnnotationMatrix`'s `to_matrix()` method now supports batched reads via the `batch_mode` argument. This functionality can also be leveraged from `SOMA`'s  `get_seurat_dimreductions_list()` and `get_seurat_dimreduction()` methods (#548).
 
 ## Changes
 
 - Decreased capacity of `AssayMatrix` arrays from 100,000 to 1,000 to improve remote-read performance (#543)
 
 ## Fixes
 
-- Don't use default assay name when recreating a `Seurat` object (thanks @dan11mcguire)
+- Don't use default assay name when recreating a `Seurat` object (thanks @dan11mcguire).
 
 # tiledbsoma 0.1.12
 

apis/r/R/SOMACollection.R

@@ -199,14 +199,48 @@ SOMACollection <- R6::R6Class(
     #' @description Convert to a [SeuratObject::Seurat] object.
     #' @param project [`SeuratObject::Project`] name for the `Seurat` object
     #' @param batch_mode logical, if `TRUE`, batch query mode is enabled for
-    #' retrieving `X`, `obsm`/`varm`, and `obsp`/`varp` layers. See
+    #' retrieving `X` layers. See
     #' [`AssayMatrix$to_dataframe()`][`AssayMatrix`] for more information.
-    to_seurat = function(project = "SeuratProject", batch_mode = FALSE) {
-      stopifnot(is_scalar_character(project))
+    #' @param somas character vector, names of `SOMA`s to include as
+    #' [`SeuratObject::Assay`]s in the `Seurat` object. If `NULL`, all `SOMA`s
+    #' are included. Can also be a named list of character vectors, where each
+    #' element corresponds to a `SOMA` name and the value is a character vector
+    #' of `X` layers from that `SOMA` to include as assays (e.g., `list("RNA" =
+    #' c("counts", "logcounts"))`).
+    to_seurat = function(
+      project = "SeuratProject",
+      somas = NULL,
+      batch_mode = FALSE
+    ) {
+      stopifnot(
+        is_scalar_character(project),
+        "'somas' must be a character vector or named list"
+          = is.null(somas) || is.character(somas) || is.list(somas)
+      )
+
+      # default list containing all somas and all layers
+      soma_list <- sapply(
+        names(self$somas),
+        FUN = function(x) c("counts", "data", "scale.data"),
+        simplify = FALSE
+      )
+
+      if (is.character(somas)) {
+        stopifnot(assert_subset(somas, names(soma_list)))
+        soma_list <- soma_list[somas]
+      } else if (is.list(somas)) {
+        stopifnot(assert_subset(names(somas), names(soma_list)))
+        soma_list <- somas
+      }
 
-      assays <- lapply(
-        X = self$somas,
-        FUN = function(x) x$to_seurat_assay(batch_mode = batch_mode)
+      assays <- mapply(
+        FUN = function(soma, layers, batch_mode) {
+          soma$to_seurat_assay(layers = layers, batch_mode = batch_mode)
+        },
+        soma = self$somas[names(soma_list)],
+        layers = soma_list,
+        MoreArgs = list(batch_mode = batch_mode),
+        SIMPLIFY = FALSE
       )
       nassays <- length(assays)
 
@@ -243,8 +277,9 @@ SOMACollection <- R6::R6Class(
       # Retrieve list of all techniques used in any soma's obsm/varm
       # dimensionality reduction arrays. The association between assay and
       # dimreduction is maintained by the DimReduc's `assay.used` slot.
-      dimreductions <- lapply(self$somas,
-        function(x) x$get_seurat_dimreductions_list(batch_mode)
+      dimreductions <- lapply(
+        self$somas,
+        function(x) x$get_seurat_dimreductions_list()
       )
       object@reductions <- Reduce(base::c, dimreductions)
 

apis/r/R/utils.R

@@ -105,7 +105,8 @@ file_path <- function(..., fsep = .Platform$file.sep) {
   file.path(..., fsep = fsep)
 }
 
-#' Assert all values of `x` are a subset of `y`. @param x,y vectors of values
+#' Assert all values of `x` are a subset of `y`.
+#' @param x,y vectors of values
 #' @param type A character vector of length 1 used in the error message
 #' @return `TRUE` if all values of `x` are present in `y`, otherwise an
 #' informative error is thrown with the missing values.

apis/r/tests/testthat/helpers.R

@@ -16,3 +16,18 @@ with_allocation_size_preference <- function(value, .local_envir = parent.frame()
   )
   tiledb::set_allocation_size_preference(value)
 }
+
+
+#' Compare data.frames or matrices after sorting dimensions
+#' Useful for comparing objects were numerically or lexicographically sorted
+#' after being reconstituted from TileDB.
+#' @noRd
+expect_equal_after_ordering_dims <- function(object, expected, ...) {
+  stopifnot(
+    is.data.frame(object) || is_matrix(object),
+    is.data.frame(expected) || is_matrix(expected)
+  )
+
+  object <- object[rownames(expected), colnames(expected)]
+  testthat::expect_equal(object, expected, ...)
+}

apis/r/tests/testthat/test_SOMACollection_Seurat.R

@@ -118,3 +118,62 @@ test_that("a dataset with empty cell identities is retrieved", {
   # Should not trigger error
   expect_silent(soco$to_seurat())
 })
+
+
+test_that("SOMAs and X layers can be subselected", {
+  tdb_uri <- withr::local_tempdir("test-multisoma-soco")
+
+  # add second assay
+  pbmc_small[["RNA2"]] <- SeuratObject::CreateAssayObject(
+    counts = SeuratObject::GetAssayData(pbmc_small[["RNA"]], "counts")
+  )
+
+  soco <- SOMACollection$new(uri = tdb_uri, verbose = TRUE)
+  soco$from_seurat(pbmc_small)
+
+  # verify both somas are present
+  expect_length(soco$somas, 2)
+
+  soco <- SOMACollection$new(uri = tdb_uri, verbose = TRUE)
+
+  # Both assays and all layers are retrieved by default
+  pbmc_small2 <- soco$to_seurat()
+  expect_setequal(
+    SeuratObject::Assays(pbmc_small2),
+    SeuratObject::Assays(pbmc_small)
+  )
+
+  expect_equal_after_ordering_dims(
+    SeuratObject::GetAssayData(pbmc_small2[["RNA"]], "counts"),
+    SeuratObject::GetAssayData(pbmc_small[["RNA"]], "counts")
+  )
+
+  expect_equal_after_ordering_dims(
+    SeuratObject::GetAssayData(pbmc_small2[["RNA"]], "data"),
+    SeuratObject::GetAssayData(pbmc_small[["RNA"]], "data")
+  )
+
+  expect_equal_after_ordering_dims(
+    SeuratObject::GetAssayData(pbmc_small2[["RNA"]], "scale.data"),
+    SeuratObject::GetAssayData(pbmc_small[["RNA"]], "scale.data")
+  )
+
+  # Only the RNA assay is retrieved
+  pbmc_small2 <- soco$to_seurat(somas = "RNA")
+  expect_equal(SeuratObject::Assays(pbmc_small2), "RNA")
+
+  # Only the RNA assay counts layer is retrieved
+  pbmc_small2 <- soco$to_seurat(somas = list(RNA = "counts"))
+  expect_equal(SeuratObject::Assays(pbmc_small2), "RNA")
+
+  # When the data layer is unset/empty it's set as identical to counts
+  expect_identical(
+    SeuratObject::GetAssayData(pbmc_small2[["RNA"]], "counts"),
+    SeuratObject::GetAssayData(pbmc_small2[["RNA"]], "data"),
+  )
+
+  expect_equal(
+    SeuratObject::GetAssayData(pbmc_small2[["RNA"]], "scale.data"),
+    new(Class = 'matrix')
+  )
+})