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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

merged 3 commits into from
Dec 6, 2023

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esiegel
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@esiegel esiegel commented Dec 3, 2023 •
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With Seurat version 5, now assays can be stored either as class Assay or Assay5. The way in which data is stored has changed between versions. This PR adds support for reading the counts sparse matrix from either formats.

fixes #22

esiegel
esiegel commented Dec 3, 2023
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DESCRIPTION Outdated
@@ -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

R/util.R
#' @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

R/util.R Outdated
# 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

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_")
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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

tests/testthat/test-util.R

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.

esiegel
esiegel commented Dec 3, 2023
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DESCRIPTION Outdated
Config/testthat/edition: 3
Imports:
methods,
Seurat,
Seurat (>= 5.0.0),
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In order to support v5 datasets, we need to bump the min version of Seurat. Also, have a direct dependency on SeuratObject because I think using the LayerData method directly reads better.

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Could we keep the Imports on Seurat unversioned and Suggests >= 5.0.0? I am not sure if Roxygen will let you specify it that way, but I imagine cutting to Seurat v5 will trigger a lot of support tickets

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Agreed, making v5 a requirement is probably going to be an issue in the near term.

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will put in effort to not make this a requirement

jsicherman
jsicherman reviewed Dec 4, 2023
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Some nits. I do think it's worth thinking about how to not require users to update to Seurat v5, as (at least to me) it is kind of a painful update with a long dependency chain

DESCRIPTION Outdated
Config/testthat/edition: 3
Imports:
methods,
Seurat,
Seurat (>= 5.0.0),
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Could we keep the Imports on Seurat unversioned and Suggests >= 5.0.0? I am not sure if Roxygen will let you specify it that way, but I imagine cutting to Seurat v5 will trigger a lot of support tickets

tests/testthat/test-util.R
Comment on lines +19 to +25
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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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.

R/util.R Outdated
# The same as using the helper `assay$counts` but less indirection.
# With Assay5 it is important to use this method as oppossed to grabbing
# the data from `assay@layers` directly as that matrix won't contain the dimnames
SeuratObject::LayerData(assay, "counts")
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Per the above suggestion about keeping Seurat dependency unversioned, you could probably...

if (unlist(packageVersion("Seurat"))[1] > 5) {
  SeuratObject::LayerData(assay, "counts")
} else {
  assay@counts
}

Although I am not sure how that would interact with NAMESPACE

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Maybe something like this:

if (packageVersion("Seurat") >= 5) {
  SeuratObject::LayerData(assay, "counts")
} else {
  if (is(assay, 'Assay5')) {
    stop("Cannot get count matrix: Please upgrade to Seurat > 5 to support dataset")
  }

  assay@counts
}

It looks like it is possible to have a Seurat object with a mix of assay versions.

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The only way they get into the else if is if they download a Seurat 5 dataset while on Seurat < 5, right? I think that is a fine condition to stop on. Make sure to unlist the return of packageVersion, though (it is a list with each entry being a corresponding x/y/z)

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that is my understanding

@esiegel esiegel merged commit 6988243 into main Dec 6, 2023
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@esiegel esiegel deleted the esiegel/support_assay5 branch December 6, 2023 18:09
@esiegel esiegel mentioned this pull request Jan 31, 2024
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@stephenwilliams22 stephenwilliams22 stephenwilliams22 approved these changes

@jsicherman jsicherman Awaiting requested review from jsicherman

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Support Assay5 assays stored in seurat objects
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@esiegel @stephenwilliams22 @jsicherman