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

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merged 3 commits into from
Dec 6, 2023
Merged

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

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f2424cd
Add support for assays stored as SeuratObject::Assay5
esiegel Dec 3, 2023
d367b88
converting large assays was too slow
esiegel Dec 3, 2023
fbdb3dc
remove strict dependency on seurat 5
esiegel Dec 5, 2023
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -14,7 +14,8 @@ Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests:
testthat (>= 3.0.0),
Matrix
Matrix,
SeuratObject
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This is used in the tests to create a Seurat dataset with a v5 assay. running devtools::check complains if we don't add this as a dependency. For test dependencies it is recommended to add these to suggests

Config/testthat/edition: 3
Imports:
methods,
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2 changes: 2 additions & 0 deletions NAMESPACE
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@@ -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)
Expand All @@ -18,6 +19,7 @@ importFrom(Seurat,Idents)
importFrom(Seurat,Reductions)
importFrom(hdf5r,H5File)
importFrom(hdf5r,H5T_STRING)
importFrom(methods,as)
importFrom(methods,is)
importFrom(utils,download.file)
importFrom(utils,packageVersion)
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3 changes: 2 additions & 1 deletion R/err.R
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Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion R/lib.R
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Expand Up @@ -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)
Expand All @@ -58,7 +59,7 @@ create_loupe_from_seurat <- function(
}

success <- create_loupe(
assay@counts,
counts,
clusters=clusters,
projections=projections,
output_dir=output_dir,
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23 changes: 22 additions & 1 deletion R/util.R
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Expand Up @@ -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)
Expand All @@ -67,6 +68,26 @@ 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

#' @importFrom methods as
#'
#' @export
counts_matrix_from_assay <- function(assay) {
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Adding this method to get the counts matrix from either of the assay versions instead of updating the select_assay method to just return the counts matrix directly. Doing this so that I don't break anyone's code if they are relying on select_assay

# convert to older format so that we can consistently access the counts matrix
# Seurat::Assay5 was introduced with Seurat-5.0 and stores the data completely differently
# within the `layers` slot.
if (is(assay, "Assay5")) {
assay <- suppressWarnings(methods::as(object = assay, Class = 'Assay'))
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During conversion using as lots of warning pop up if the assay is missing fields even thought the conversion still succeeds.

Another alternative would be to do something like assay@layers[["counts"]] as it seems this is where the counts matrix is stored. By using the as conversion method we don't have to worry if the location changes.

conversion logic can be seen here

}

assay@counts
}

#' Select clusters from the assay
#'
#' @param obj A Seurat Object
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5 changes: 4 additions & 1 deletion README.md
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Expand Up @@ -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)
)
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17 changes: 17 additions & 0 deletions man/counts_matrix_from_assay.Rd
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24 changes: 19 additions & 5 deletions tests/testthat/test-util.R
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Expand Up @@ -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_")
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Unrelated change, but the names here didn't need to have an underscore even though the key parameter to CreateAssayObject requires it

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_")
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The Seurat package doesn't export the underlying v5 create method like it does with the non v5.

Comment on lines +19 to +25
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Suggested change
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_")
rna <- create_count_mat(5, 5)
obj <- Seurat::CreateSeuratObject(rna, assay="rna1")
obj[["rna2"]] = Seurat::CreateAssayObject(rna, key="rna2_")
obj[["rna3"]] = SeuratObject::CreateAssay5Object(rna, key="rna3_")

R will pass function arguments by value rather than reference so you shouldn't need to construct multiple instances yourself

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I actually want to create three different matrices because I want their values to be different for the tests. Turns out R is copy by value, but only if the value is modified.


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", {
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