Merge pull request #3548 from satijalab/develop

Seurat v3.2.2

.github/ISSUE_TEMPLATE/analysis-question.md

@@ -0,0 +1,12 @@
+---
+name: "❓Analysis question"
+about: Ask a question about the analysis of single-cell data
+title: ''
+labels: question
+assignees: ''
+
+---
+
+<!-- Please search the previous issues for similar questions before opening a new issue. If there are similar previous issues, please reference them in your issue (https://help.github.com/en/github/writing-on-github/autolinked-references-and-urls) -->
+
+<!-- Please clearly explain your question and include all relevant code. Please ensure that code is formatted correctly: https://help.github.com/en/github/writing-on-github/creating-and-highlighting-code-blocks -->

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,20 @@
+---
+name: "\U0001F41BBug report"
+about: Describe a bug you've seen with a reproducible example
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+<!-- Briefly describe your problem and what output you expect. If you have a question, please use the analysis question template instead. -->
+
+<!-- Before posting an issue, ensure that the bug is reproducible by re-running the code that produced the issue in a new R session.-->
+
+<!-- Please include a minimal reproducible code example. You can use the small test data included in Seurat (`pbmc_small`) to demonstrate the issue, or a public dataset (for example, a dataset available through SeuratData https://github.com/satijalab/seurat-data). If you cannot reproduce the issue using a public dataset, please still provide code that reproduces the issue on your data and we will try to address it. -->
+
+<!-- Please include the output of `sessionInfo()` and your operating system in your issue. -->
+
+```r
+# insert reproducible example here
+```

.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,10 @@
+---
+name: "\U0001F4DADocumentation"
+about: An issue related to documentation at https://satijalab.org/seurat/
+title: ''
+labels: documentation
+assignees: ''
+
+---
+
+<!-- A clear description of what content at https://satijalab.org/seurat or in the Seurat function man pages is an issue. -->

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,10 @@
+---
+name: "\U0001F680Feature request"
+about: Request a new feature
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+<!-- Kindly explain the new feature you would like and why this would be useful. -->

.gitignore

@@ -7,4 +7,3 @@ src/*.so
 src/*.dll
 .DS_Store
 *.pdf
-*.Rproj

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.2.1
-Date: 2020-09-04
+Version: 3.2.2
+Date: 2020-09-25
 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 Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
 Authors@R: c(
@@ -58,7 +58,7 @@ Imports:
     rsvd,
     Rtsne,
     scales,
-    sctransform (>= 0.2.0),
+    sctransform (>= 0.3.0),
     shiny,
     spatstat,
     stats,

NAMESPACE

@@ -468,6 +468,7 @@ importFrom(cowplot,plot_grid)
 importFrom(cowplot,theme_cowplot)
 importFrom(fitdistrplus,fitdist)
 importFrom(future,nbrOfWorkers)
+importFrom(future,plan)
 importFrom(future.apply,future_lapply)
 importFrom(future.apply,future_sapply)
 importFrom(ggplot2,Geom)

NEWS.md

@@ -2,6 +2,14 @@
 All notable changes to Seurat will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 
+## [3.2.2] - 2020-09-25
+### Changes
+- Set the seed in `WhichCells` regardless of whether or not `idents` is passed
+- Retain Graph and Neighbor objects when subsetting only on features
+- Fix data.frame input to `CreateAssayObject()` when data.frame has no rownames.
+- Default annoy search to sequential if not using multicore future plans.
+- Require sctransform >= 0.3.0
+
 ## [3.2.1] - 2020-09-04
 ### Added
 - Added support for nearest neighbor input and `return.model` parameter in `RunUMAP()`

R/clustering.R

@@ -553,12 +553,18 @@ AnnoyBuildIndex <- function(data, metric = "euclidean", n.trees = 50) {
 # @param search.k During the query it will inspect up to search_k nodes which
 # gives you a run-time tradeoff between better accuracy and speed.
 # @ param include.distance Include the corresponding distances
+#' @importFrom future plan
+#' @importFrom future.apply future_lapply
 #
 AnnoySearch <- function(index, query, k, search.k = -1, include.distance = TRUE) {
   n <- nrow(x = query)
   idx <- matrix(nrow = n,  ncol = k)
   dist <- matrix(nrow = n, ncol = k)
   convert <- methods::is(index, "Rcpp_AnnoyAngular")
+  if (!inherits(x = plan(), what = "multicore")) {
+    oplan <- plan(strategy = "sequential")
+    on.exit(plan(oplan), add = TRUE)
+  }
   res <- future_lapply(X = 1:n, FUN = function(x) {
     res <- index$getNNsByVectorList(query[x, ], k, search.k, include.distance)
     # Convert from Angular to Cosine distance

R/dimensional_reduction.R

@@ -1133,7 +1133,7 @@ RunUMAP.default <- function(
   reduction.key = 'UMAP_',
   assay = NULL,
   reduction.model = NULL,
-  return.model = FALSE, 
+  return.model = FALSE,
   umap.method = 'uwot',
   n.neighbors = 30L,
   n.components = 2L,
@@ -1270,7 +1270,7 @@ RunUMAP.default <- function(
           a = a,
           b = b,
           fast_sgd = uwot.sgd,
-          verbose = verbose, 
+          verbose = verbose,
           ret_model = return.model
         )
       }
@@ -1303,16 +1303,16 @@ RunUMAP.default <- function(
       if (is.list(x = object)) {
         if (packageVersion(pkg = "uwot") <= '0.1.8.9000') {
           stop("This uwot functionality requires uwot version >= 0.1.8.9000",
-               "Installing the latest version from github can be done with", 
+               "Installing the latest version from github can be done with",
                "remotes::install_github('jlmelville/uwot')")
         }
         uwot::umap_transform(
           X = NULL,
-          nn_method = object, 
-          model = model, 
+          nn_method = object,
+          model = model,
           n_threads = nbrOfWorkers(),
           n_epochs = n.epochs,
-          verbose = verbose 
+          verbose = verbose
         )
       } else {
         umap_transform(
@@ -1450,7 +1450,7 @@ RunUMAP.Graph <- function(
 #' @param assay Assay to pull data for when using \code{features}, or assay used to construct Graph
 #' if running UMAP on a Graph
 #' @param nn.name Name of knn output on which to run UMAP
-#' @param slot The slot used to pull data for when using \code{features}. data slot is by default. 
+#' @param slot The slot used to pull data for when using \code{features}. data slot is by default.
 #' @param umap.method UMAP implementation to run. Can be
 #' \describe{
 #'   \item{\code{uwot}:}{Runs umap via the uwot R package}
@@ -1521,11 +1521,11 @@ RunUMAP.Seurat <- function(
   features = NULL,
   graph = NULL,
   assay = DefaultAssay(object = object),
-  nn.name = NULL, 
+  nn.name = NULL,
   slot = 'data',
   umap.method = 'uwot',
   reduction.model = NULL,
-  return.model = FALSE, 
+  return.model = FALSE,
   n.neighbors = 30L,
   n.components = 2L,
   metric = 'cosine',

R/generics.R

@@ -72,13 +72,13 @@ as.loom <- function(x, ...) {
 }
 
 #' Convert objects to Neighbor ojbects
-#' 
+#'
 #' @param x An object to convert to \code{Neighbor}
 #' @param ... Arguments passed to other methods
-#' 
+#'
 #' @rdname as.Neighbor
 #' @export as.Neighbor
-#' 
+#'
 as.Neighbor <- function(x, ...) {
   UseMethod(generic = 'as.Neighbor', object = x)
 }
@@ -550,8 +550,8 @@ Idents <- function(object, ... ) {
   UseMethod(generic = 'Idents<-', object = object)
 }
 
-#' Get Neighbor algorithm index 
-#' 
+#' Get Neighbor algorithm index
+#'
 #' @param object An object
 #' @param ... Arguments passed to other methods;
 #'
@@ -577,7 +577,7 @@ Index <- function(object, ...) {
 }
 
 #' Get Neighbor nearest neighbor index matrices
-#' 
+#'
 #' @param object An object
 #' @param ... Arguments passed to other methods;
 #'
@@ -1180,7 +1180,7 @@ SetIdent <- function(object, ...) {
 }
 
 #' Get spatially variable feature information
-#' 
+#'
 #' @rdname SpatiallyVariableFeatures
 #' @export SpatiallyVariableFeatures
 #'