Merge pull request #4529 from satijalab/develop

Seurat v4.0.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.1
-Date: 2021-03-17
+Version: 4.0.2
+Date: 2021-05-20
 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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(
@@ -10,7 +10,7 @@ Authors@R: c(
   person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"),
   person(given = "Christoph", family = "Hafemeister", email = "chafemeister@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
   person(given = "Yuhan", family = "Hao", email = "yhao@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
-  person(given = "Paul", family = "Hoffman", email = "nygcSatijalab@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
+  person(given = "Paul", family = "Hoffman", email = "seurat@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
   person(given = "Jaison", family = "Jain", email = "jjain@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
   person(given = "Efthymia", family = "Papalexi", email = "epapalexi@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
   person(given = "Patrick", family = "Roelli", email = "proelli@nygenome.org", role = "ctb"),

NAMESPACE

@@ -117,6 +117,7 @@ export("Project<-")
 export("SCTResults<-")
 export("Tool<-")
 export("VariableFeatures<-")
+export(AddAzimuthResults)
 export(AddMetaData)
 export(AddModuleScore)
 export(AggregateExpression)
@@ -360,6 +361,7 @@ importFrom(MASS,lda)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,colMeans)
 importFrom(Matrix,colSums)
+importFrom(Matrix,crossprod)
 importFrom(Matrix,readMM)
 importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
@@ -492,6 +494,7 @@ importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,layer)
+importFrom(ggplot2,layer_scales)
 importFrom(ggplot2,margin)
 importFrom(ggplot2,position_dodge)
 importFrom(ggplot2,position_jitterdodge)

NEWS.md

@@ -1,3 +1,28 @@
+# Seurat 4.0.2 (2020-03-20)
+## Added
+- New `AddAzimuthScores()` and `AddAzimuthResults()` functions
+- Add `shuffle` parameter to `FeatureScatter()` ([#4280](https://github.com/satijalab/seurat/pull/4280))
+- Add `lsiproject` and `rpca` options for `FindTransferAnchors()`
+- Add `rlsi` option for `FindIntegrationAnchors()`
+
+## Changes
+- Preserve feature metadata when converting from `SingleCellExperiment` to `SeuratObject` class
+([#4205](https://github.com/satijalab/seurat/issues/4205))
+- Preserve multiple assays when converting from `SingleCellExperiment` to `SeuratObject` class
+([#3764](https://github.com/satijalab/seurat/issues/3764))
+- Fix passing of `score.thresh` parameter in `ScoreJackStraw()` ([#4268](https://github.com/satijalab/seurat/pull/4268))
+- Fix FC calculation in `FindMarkers()` non-log transformed data.
+- Add umap-learn version >= 0.5.0 compatibility for `RunUMAP()`
+- Fix `DotPlot` to use `log1p` when `scale=False`
+([#4298](https://github.com/satijalab/seurat/issues/4298))
+- Fix split and shuffled `DimPlot`
+- Disallow NULL or another length 0 vector for `ident.1` in `FindMarkers()`
+- Fix range shift when labeling clusters on a GeomSpatial plot
+- Fix SpatialPlot distortion for non-square images.
+- Fix future-related warnings in `FindIntegrationAnchors()`
+- Fix `fc.name` parameter in `FindMarkers()` ([#4474](https://github.com/satijalab/seurat/issues/4474))
+- Deprecate `group.by` parameter in `PlotPerturbScore()` in favor of `mixscape.class`.
+
 # Seurat 4.0.1 (2020-03-17)
 ## Added
 - Add direction option to `PlotClusterTree()`

R/differential_expression.R

@@ -813,6 +813,9 @@ FindMarkers.Seurat <- function(
   if (!is.null(x = assay) && !is.null(x = reduction)) {
     stop("Please only specify either assay or reduction.")
   }
+  if (length(x = ident.1) == 0) {
+    stop("At least 1 ident must be specified in `ident.1`")
+  }
   # select which data to use
   if (is.null(x = reduction)) {
     assay <- assay %||% DefaultAssay(object = object)
@@ -836,6 +839,20 @@ FindMarkers.Seurat <- function(
       cells = c(cells$cells.1, cells$cells.2)
     )
   }
+  # check normalization method
+  norm.command <- paste0("NormalizeData.", assay)
+  if (norm.command %in% Command(object = object) && is.null(x = reduction)) {
+    norm.method <- Command(
+      object = object,
+      command = norm.command,
+      value = "normalization.method"
+    )
+    if (norm.method != "LogNormalize") {
+      mean.fxn <- function(x) {
+        return(log(x = rowMeans(x = x) + pseudocount.use, base = base))
+      }
+    }
+  }
   de.results <- FindMarkers(
     object = data.use,
     slot = slot,
@@ -856,6 +873,7 @@ FindMarkers.Seurat <- function(
     pseudocount.use = pseudocount.use,
     mean.fxn = mean.fxn,
     base = base,
+    fc.name = fc.name,
     ...
   )
   return(de.results)
@@ -1617,9 +1635,7 @@ MarkerTest <- function(
 # @param data.use Data to test
 # @param cells.1 Group 1 cells
 # @param cells.2 Group 2 cells
-# @param latent.vars Confounding variables to adjust for in DE test. Default is
-# "nUMI", which adjusts for cellular depth (i.e. cellular detection rate). For
-# non-UMI based data, set to nGene instead.
+# @param latent.vars Confounding variables to adjust for in DE test
 # @param verbose print output
 # @param \dots Additional parameters to zero-inflated regression (zlm) function
 # in MAST
@@ -1630,17 +1646,6 @@ MarkerTest <- function(
 # genes.
 #
 #' @importFrom stats relevel
-#
-# @export
-#
-# @examples
-# \dontrun{
-#   data("pbmc_small")
-#   pbmc_small
-#   MASTDETest(pbmc_small, cells.1 = WhichCells(object = pbmc_small, idents = 1),
-#               cells.2 = WhichCells(object = pbmc_small, idents = 2))
-# }
-#
 MASTDETest <- function(
   data.use,
   cells.1,

R/dimensional_reduction.R

@@ -1433,7 +1433,7 @@ RunUMAP.Graph <- function(
   reduction.key = 'UMAP_',
   ...
 ) {
-  CheckDots(...)
+  #CheckDots(...)
   if (umap.method != 'umap-learn') {
     warning(
       "Running UMAP on Graph objects is only supported using the umap-learn method",
@@ -1465,7 +1465,7 @@ RunUMAP.Graph <- function(
   b <- b %||% ab.params[[2]]
   n.epochs <- n.epochs %||% 0L
   random.state <- sklearn$utils$check_random_state(seed = as.integer(x = seed.use))
-  embeddings <- umap$umap_$simplicial_set_embedding(
+  umap.args <- list(
     data = data,
     graph = object,
     n_components = n.components,
@@ -1481,6 +1481,18 @@ RunUMAP.Graph <- function(
     metric_kwds = metric.kwds,
     verbose = verbose
   )
+  if (numeric_version(x = umap$pkg_resources$get_distribution("umap-learn")$version) >=
+      numeric_version(x = "0.5.0")) {
+    umap.args <- c(umap.args, list(
+      densmap = FALSE,
+      densmap_kwds = NULL,
+      output_dens = FALSE
+    ))
+  }
+  embeddings <- do.call(what = umap$umap_$simplicial_set_embedding, args = umap.args)
+  if (length(x = embeddings) == 2) {
+    embeddings <- embeddings[[1]]
+  }
   rownames(x = embeddings) <- colnames(x = data)
   colnames(x = embeddings) <- paste0("UMAP_", 1:n.components)
   # center the embeddings on zero
@@ -1658,9 +1670,9 @@ RunUMAP.Seurat <- function(
     if (!inherits(x = object[[nn.name]], what = "Neighbor")) {
       stop(
         "Please specify a Neighbor object name, ",
-        "instead of the name of a ", 
-        class(object[[nn.name]]), 
-        " object",   
+        "instead of the name of a ",
+        class(object[[nn.name]]),
+        " object",
         call. = FALSE
       )
     }
@@ -1669,9 +1681,9 @@ RunUMAP.Seurat <- function(
     if (!inherits(x = object[[graph]], what = "Graph")) {
       stop(
         "Please specify a Graph object name, ",
-        "instead of the name of a ", 
-        class(object[[graph]]), 
-        " object",   
+        "instead of the name of a ",
+        class(object[[graph]]),
+        " object",
         call. = FALSE
       )
     }
@@ -1764,7 +1776,7 @@ ScoreJackStraw.DimReduc <- function(object, dims = 1:5, score.thresh = 1e-5, ...
   JS(object = object) <- ScoreJackStraw(
     object = JS(object = object),
     dims = dims,
-    score.thresh = 1e-5,
+    score.thresh = score.thresh,
     ...
   )
   return(object)
@@ -1792,6 +1804,7 @@ ScoreJackStraw.Seurat <- function(
   object[[reduction]] <- ScoreJackStraw(
     object = object[[reduction]],
     dims = dims,
+    score.thresh = score.thresh,
     ...
   )
   if (do.plot) {