Merge branch 'develop' into master

0CBH0 · Feb 25, 2020 · 841013d · 841013d
2 parents 94f8200 + 9648dd0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.1.3
-Date: 2020-02-07
+Version: 3.1.4
+Date: 2020-02-21
 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.
 Authors@R: c(
@@ -43,6 +43,7 @@ Imports:
     MASS,
     Matrix (>= 1.2-14),
     metap,
+    patchwork,
     pbapply,
     plotly,
     png,

diff --git a/NAMESPACE b/NAMESPACE
@@ -482,6 +482,7 @@ importFrom(methods,setOldClass)
 importFrom(methods,signature)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
+importFrom(patchwork,wrap_plots)
 importFrom(pbapply,pbapply)
 importFrom(pbapply,pblapply)
 importFrom(pbapply,pbsapply)

diff --git a/NEWS.md b/NEWS.md
@@ -2,7 +2,12 @@
 All notable changes to Seurat will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 
-## [3.1.3] = 2020-02-07
+## [3.1.4] - 2020-02-20
+### Changes 
+- Fixes to `DoHeatmap` to remain compatible with ggplot2 v3.3
+- Adoption of `patchwork` framework to replace `CombinePlots`
+
+## [3.1.3] - 2020-02-07
 ### Added
 - New system agnostic `Which` function to address problems with FItSNE on Windows
 

diff --git a/R/convenience.R b/R/convenience.R
@@ -19,6 +19,8 @@ PCHeatmap <- function(object, ...) {
   return(do.call(what = 'DimHeatmap', args = args))
 }
 
+#' @param ... Extra parameters passed to \code{DimPlot}
+#'
 #' @rdname DimPlot
 #' @export
 #'

diff --git a/R/objects.R b/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"))

diff --git a/R/preprocessing.R b/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