Merge pull request satijalab#260 from satijalab/fix/SCTMerge

Fix for multi-sct merges

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 3.1.3.9003
+Version: 3.1.3.9004
 Date: 2020-02-13
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.

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