Merge branch 'develop' into feat/ObjectUpdates

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 3.1.0.9010
+Version: 3.1.0.9012
 Date: 2019-09-17
 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/dimensional_reduction.R

@@ -1152,6 +1152,7 @@ RunUMAP.default <- function(
   negative.sample.rate = 5,
   a = NULL,
   b = NULL,
+  uwot.sgd = FALSE,
   seed.use = 42,
   metric.kwds = NULL,
   angular.rp.forest = FALSE,
@@ -1162,7 +1163,6 @@ RunUMAP.default <- function(
   CheckDots(...)
   if (!is.null(x = seed.use)) {
     set.seed(seed = seed.use)
-    py_set_seed(seed = seed.use)
   }
   if (umap.method != 'umap-learn' && getOption('Seurat.warn.umap.uwot', TRUE)) {
     warning(
@@ -1180,6 +1180,9 @@ RunUMAP.default <- function(
       if (!py_module_available(module = 'umap')) {
         stop("Cannot find UMAP, please install through pip (e.g. pip install umap-learn).")
       }
+      if (!is.null(x = seed.use)) {
+        py_set_seed(seed = seed.use)
+      }
       if (typeof(x = n.epochs) == "double") {
         n.epochs <- as.integer(x = n.epochs)
       }
@@ -1229,6 +1232,7 @@ RunUMAP.default <- function(
         negative_sample_rate = negative.sample.rate,
         a = a,
         b = b,
+        fast_sgd = uwot.sgd,
         verbose = verbose
       )
     },
@@ -1268,6 +1272,7 @@ RunUMAP.Graph <- function(
   negative.sample.rate = 5L,
   a = NULL,
   b = NULL,
+  uwot.sgd = FALSE,
   seed.use = 42L,
   metric.kwds = NULL,
   verbose = TRUE,
@@ -1383,6 +1388,7 @@ RunUMAP.Graph <- function(
 #' @param b More specific parameters controlling the embedding. If NULL, these values are set
 #' automatically as determined by min. dist and spread. Parameter of differentiable approximation of
 #' right adjoint functor.
+#' @param uwot.sgd Set \code{uwot::umap(fast_sgd = TRUE)}; see \code{\link[uwot]{umap}} for more details
 #' @param metric.kwds A dictionary of arguments to pass on to the metric, such as the p value for
 #' Minkowski distance. If NULL then no arguments are passed on.
 #' @param angular.rp.forest Whether to use an angular random projection forest to initialise the
@@ -1421,6 +1427,7 @@ RunUMAP.Seurat <- function(
   negative.sample.rate = 5L,
   a = NULL,
   b = NULL,
+  uwot.sgd = FALSE,
   seed.use = 42L,
   metric.kwds = NULL,
   angular.rp.forest = FALSE,
@@ -1460,6 +1467,7 @@ RunUMAP.Seurat <- function(
     negative.sample.rate = negative.sample.rate,
     a = a,
     b = b,
+    uwot.sgd = uwot.sgd,
     seed.use = seed.use,
     metric.kwds = metric.kwds,
     angular.rp.forest = angular.rp.forest,

R/preprocessing.R

@@ -489,7 +489,7 @@ GetResidual <- function(
       x = new_features,
       y = vst_set_genes
     )
-    if (diff_features !=0){
+    if (length(x = diff_features) !=0) {
       warning(
         "The following ", length(x = diff_features),
         " features do not exist in all SCT models: ",
@@ -535,9 +535,11 @@ GetResidual <- function(
       object = object,
       assay = assay,
       slot = "scale.data",
-      new.data = new.scale.data
+      new.data = rbind(
+        GetAssayData(object = object, slot = 'scale.data', assay = assay),
+        new.scale.data
+      )
     )
-
     }
   }
   }