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bindCOLS error workaround in runMultiUMAP function #7

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Sep 28, 2024
Merged

bindCOLS error workaround in runMultiUMAP function #7

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7 changes: 7 additions & 0 deletions R/runMultiUMAP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -88,11 +88,18 @@ setGeneric("calculateMultiUMAP", function(x, ...) standardGeneric("calculateMult
#' @rdname runMultiUMAP
#' @importFrom utils head
#' @importFrom uwot umap
#' @importFrom DelayedArray DelayedArray
setMethod("calculateMultiUMAP", "ANY", function(x, ..., metric="euclidean") {
if (length(x)==0) {
stop("'x' must contain one or more matrices")
}
mult.metrics <- .compute_multi_modal_metrics(x, metric=metric)

# Work around Bioconductor/DelayedArray#100 for the time being.
if (any(vapply(x, is, class="DelayedArray", TRUE))) {
x <- lapply(x, DelayedArray)
}

combined <- as.matrix(do.call(cbind, x))
umap(combined, metric=mult.metrics, ...)
})
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20 changes: 20 additions & 0 deletions tests/testthat/test-multi-umap.R
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Expand Up @@ -28,3 +28,23 @@ test_that("multi-modal UMAP works as expected", {
output2 <- runMultiUMAP(sce, assays=1, dimreds=1, altexps=1, altexp.assay=1, n_components=10)
expect_identical(output, reducedDim(output2, "MultiUMAP"))
})

test_that("multi-modal UMAP works with mixed DelayedArrays and matrices", {
set.seed(9999)
output1 <- calculateMultiUMAP(things)

set.seed(9999)
output2 <- calculateMultiUMAP(lapply(things, DelayedArray::DelayedArray))
expect_identical(output1, output2)

# Same result for SCEs.
sce <- SingleCellExperiment(list(X=DelayedArray::DelayedArray(t(stuff))),
reducedDims=list(Y=stuff[,1:5]), altExps=list(Z=SummarizedExperiment(t(stuff[,1:20]))))

set.seed(9999)
output3 <- calculateMultiUMAP(things, n_components=10)

set.seed(9999)
output4 <- runMultiUMAP(sce, assays=1, dimreds=1, altexps=1, altexp.assay=1, n_components=10)
expect_identical(output3, reducedDim(output4, "MultiUMAP"))
})