fix: preserve assay dimnames in normalization

GuangchuangYu · GuangchuangYu · commit bdef4ef450c8 · 2026-05-25T08:39:38.000+08:00
diff --git a/R/preprocessing.R b/R/preprocessing.R
@@ -70,6 +70,7 @@ NormalizeData <- function(object, scale.factor = 10000) {
         )
     }
     logcounts <- log1p(logcounts)
+    dimnames(logcounts) <- dimnames(object)
     SummarizedExperiment::assay(object, "logcounts") <- logcounts
     object <- sclet_restore_state(object, prev_state)
     object <- sclet_set_layer(object, name = "counts", assay = "counts", role = "counts", active = FALSE)

Original file line number	Diff line number	Diff line change
`@@ -70,6 +70,7 @@ NormalizeData <- function(object, scale.factor = 10000) {`
`70`	`70`	`)`
`71`	`71`	`}`
`72`	`72`	`logcounts <- log1p(logcounts)`
	`73`	`+ dimnames(logcounts) <- dimnames(object)`
`73`	`74`	`SummarizedExperiment::assay(object, "logcounts") <- logcounts`
`74`	`75`	`object <- sclet_restore_state(object, prev_state)`
`75`	`76`	`object <- sclet_set_layer(object, name = "counts", assay = "counts", role = "counts", active = FALSE)`