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...
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...
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@@ -360,7 +360,7 @@ runSoupX <- function(inSCE,
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360
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360
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out <- SoupX::adjustCounts(sc, method = adjustMethod,
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361
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roundToInt = roundToInt, tol = tol, pCut = pCut)
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message(paste0(date(), " ... Generating UMAP"))
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363
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- inSCE <- runQuickUMAP(inSCE, useAssay = useAssay,
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363
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+ inSCE <- runQuickUMAP(inSCE, useAssay = useAssay, sample = NULL,
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364
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reducedDimName = "sampleUMAP")
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365
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365
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return(list(sc = sc, out = out,
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366
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366
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umap = SingleCellExperiment::reducedDim(inSCE, "sampleUMAP")))
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