fix for multi-sct merges

R/objects.R

@@ -5667,19 +5667,24 @@ merge.Assay <- function(
   if (all(IsSCT(assay = assays))) {
     vst.set.new <- list()
     idx <- 1
+    umi.assay.new <- list()
     for (i in 1:length(x = assays)) {
       vst.set.old <- Misc(object = assays[[i]], slot = "vst.set")
+      umi.assay.old <- Misc(object = assays[[i]], slot = "umi.assay")
       if (!is.null(x = vst.set.old)) {
         for (j in 1:length(x = vst.set.old)) {
           vst.set.new[[idx]] <- vst.set.old[[j]]
+          umi.assay.new[[idx]] <- umi.assay.old[[j]]
           idx <- idx + 1
         }
       } else if (!is.null(x = Misc(object = assays[[i]], slot = "vst.out"))) {
         vst.set.new[[idx]] <- Misc(object = assays[[i]], slot = "vst.out")
+        umi.assay.new[[idx]] <- Misc(object = assays[[i]], slot = "umi.assay")
         idx <- idx + 1
       }
     }
     Misc(object = combined.assay, slot = "vst.set") <- vst.set.new
+    Misc(object = combined.assay, slot = "umi.assay") <- umi.assay.new
     scale.data <- do.call(
       what = cbind,
       args = lapply(X = assays, FUN = function(x) GetAssayData(object = x, slot = "scale.data"))

R/preprocessing.R

@@ -453,14 +453,16 @@ GetResidual <- function(
   object,
   features,
   assay = "SCT",
-  umi.assay = "RNA",
+  umi.assay = NULL,
   clip.range = NULL,
   replace.value = FALSE,
   verbose = TRUE
 ) {
   if (!IsSCT(assay = object[[assay]])) {
     stop(assay, " assay was not generated by SCTransform")
   }
+  umi.assay <- umi.assay %||% Misc(object = object[[assay]], slot = "umi.assay")
+  umi.assay <- umi.assay %||% "RNA" # for object created in 3.1.1 or earlier, default to RNA
   if (replace.value) {
     new_features <- features
   } else {
@@ -534,7 +536,7 @@ GetResidual <- function(
       object.v <- GetResidualVstOut(
         object = object.v,
         assay = assay,
-        umi.assay = umi.assay,
+        umi.assay = umi.assay[[v]],
         new_features = new_features,
         vst_out = vst_out,
         clip.range = clip.range,
@@ -1353,6 +1355,7 @@ SCTransform <- function(
   # save clip.range into vst model
   vst.out$arguments$sct.clip.range <- clip.range
   Misc(object = assay.out, slot = 'vst.out') <- vst.out
+  Misc(object = assay.out, slot = 'umi.assay') <- assay
   # also put gene attributes in meta.features
   assay.out[[paste0('sct.', names(x = vst.out$gene_attr))]] <- vst.out$gene_attr
   assay.out[['sct.variable']] <- rownames(x = assay.out[[]]) %in% top.features