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@@ -552,7 +552,9 @@ featureModuleTable <- function(sce,
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552
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552
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useAssay = useAssay,
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553
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553
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altExpName = altExpName,
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554
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type = "proportion")
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555
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- allGenes <- topRank(factorizeMatrix$proportions$module, n = nrow(sce))
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555
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+ altExp <- SingleCellExperiment::altExp(sce, altExpName)
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+
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557
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+ allGenes <- topRank(factorizeMatrix$proportions$module, n = nrow(altExp))
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556
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maxlen <- max(vapply(allGenes$names, length, integer(1)))
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557
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559
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558
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560
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if (is.null(displayName)) {
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@@ -563,7 +565,7 @@ featureModuleTable <- function(sce,
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563
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565
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} else {
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564
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566
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dn <- lapply(allGenes$index,
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565
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567
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FUN = function(v) {
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566
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- SummarizedExperiment::rowData(sce)[[displayName]][v]
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568
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+ SummarizedExperiment::rowData(altExp)[[displayName]][v]
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567
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569
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})
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568
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570
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res <- vapply(dn,
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569
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571
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FUN = "[",
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