Merge pull request #7847 from satijalab/develop

Seurat v4.4.0
satijalab · Sep 28, 2023 · 57564e2 · 57564e2
2 parents ba30617 + d9f09de
commit 57564e2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.3.0
-Date: 2022-11-18
+Version: 4.4.0
+Date: 2023-09-26
 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(
@@ -58,6 +58,7 @@ Imports:
     plotly (>= 4.9.0),
     png,
     progressr,
+    purrr,
     RANN,
     RColorBrewer,
     Rcpp (>= 1.0.7),
@@ -67,9 +68,9 @@ Imports:
     ROCR,
     Rtsne,
     scales,
-    scattermore (>= 0.7),
-    sctransform (>= 0.3.5),
-    SeuratObject (>= 4.1.3),
+    scattermore (>= 1.2),
+    sctransform (>= 0.4.0),
+    SeuratObject (>= 4.1.4),
     shiny,
     spatstat.explore,
     spatstat.geom,
@@ -98,7 +99,7 @@ Collate:
     'tree.R'
     'utilities.R'
     'zzz.R'
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 Suggests:
     ape,

diff --git a/NAMESPACE b/NAMESPACE
@@ -32,6 +32,7 @@ S3method(FindVariableFeatures,Seurat)
 S3method(FindVariableFeatures,default)
 S3method(FoldChange,Assay)
 S3method(FoldChange,DimReduc)
+S3method(FoldChange,SCTAssay)
 S3method(FoldChange,Seurat)
 S3method(FoldChange,default)
 S3method(GetAssay,Seurat)
@@ -235,6 +236,7 @@ export(LinkedFeaturePlot)
 export(Load10X_Spatial)
 export(LoadAkoya)
 export(LoadAnnoyIndex)
+export(LoadCurioSeeker)
 export(LoadHuBMAPCODEX)
 export(LoadNanostring)
 export(LoadSTARmap)
@@ -282,6 +284,7 @@ export(Radius)
 export(Read10X)
 export(Read10X_Image)
 export(Read10X_h5)
+export(Read10X_probe_metadata)
 export(ReadAkoya)
 export(ReadMtx)
 export(ReadNanostring)
@@ -402,6 +405,7 @@ importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
 importFrom(Matrix,sparse.model.matrix)
 importFrom(Matrix,sparseMatrix)
+importFrom(Matrix,summary)
 importFrom(Matrix,t)
 importFrom(RANN,nn2)
 importFrom(RColorBrewer,brewer.pal)
@@ -670,6 +674,7 @@ importFrom(plotly,plot_ly)
 importFrom(plotly,raster2uri)
 importFrom(png,readPNG)
 importFrom(progressr,progressor)
+importFrom(purrr,imap)
 importFrom(reticulate,import)
 importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_seed)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,19 @@
+# Seurat 4.4.0 (2023-09-27)
+
+## Added
+- Added parallelization support with speed improvements for `PrepSCTFindMarkers` 
+- Fix bug in `LoadNanostring`([#7566](https://github.com/satijalab/seurat/pull/7566))
+
+## Changes
+- Fix bug in `as.Seurat.SingleCellExperiment()` ([#6692](https://github.com/satijalab/seurat/issues/6692))
+- Support for Visium probe information introduced in Spaceranger 2.1 ([#7141](https://github.com/satijalab/seurat/pull/7141))
+- Add `LoadCurioSeeker` to load sequencing-based spatial datasets generated using the Curio Seeker 
+- Fix fold change calculation for assays ([#7095](https://github.com/satijalab/seurat/issues/7095))
+- Fix `pt.size` bug when rasterization is set to true ([#7379](https://github.com/satijalab/seurat/issues/7379)) 
+- Fix `FoldChange` and `FindMarkers` to support all normalization approaches ([#7115](https://github.com/satijalab/seurat/pull/7115),[#7110](https://github.com/satijalab/seurat/issues/7110),[#7095](https://github.com/satijalab/seurat/issues/7095),[#6976](https://github.com/satijalab/seurat/issues/6976),[#6654](https://github.com/satijalab/seurat/issues/6654),[#6701](https://github.com/satijalab/seurat/issues/6701),[#6773](https://github.com/satijalab/seurat/issues/6773), [#7107](https://github.com/satijalab/seurat/issues/7107))
+- Fix for handling newer ParseBio formats in `ReadParseBio` ([#7565](https://github.com/satijalab/seurat/pull/7565))
+- Fix for handling rasterization by default ([#7842](https://github.com/satijalab/seurat/pull/7842))
+
 # Seurat 4.3.0 (2022-11-18)
 
 ## Added

diff --git a/R/convenience.R b/R/convenience.R
@@ -201,7 +201,10 @@ LoadXenium <- function(data.dir, fov = 'fov', assay = 'Xenium') {
   )
 
   xenium.obj <- CreateSeuratObject(counts = data$matrix[["Gene Expression"]], assay = assay)
-  xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]])
+  if("Blank Codeword" %in% names(data$matrix))
+    xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]])
+  else
+    xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Unassigned Codeword"]])
   xenium.obj[["ControlCodeword"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Codeword"]])
   xenium.obj[["ControlProbe"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Probe"]])
 
@@ -296,6 +299,7 @@ SpatialFeaturePlot <- function(
   images = NULL,
   crop = TRUE,
   slot = 'data',
+  keep.scale = "feature",
   min.cutoff = NA,
   max.cutoff = NA,
   ncol = NULL,
@@ -313,6 +317,7 @@ SpatialFeaturePlot <- function(
     images = images,
     crop = crop,
     slot = slot,
+    keep.scale = keep.scale,
     min.cutoff = min.cutoff,
     max.cutoff = max.cutoff,
     ncol = ncol,
@@ -386,7 +391,8 @@ SpecificDimPlot <- function(object, ...) {
 #' @export
 #'
 ReadParseBio <- function(data.dir, ...) {
-  mtx <- file.path(data.dir, "DGE.mtx")
+  file.dir <- list.files(path = data.dir, pattern = ".mtx")
+  mtx <- file.path(data.dir, file.dir)
   cells <- file.path(data.dir, "cell_metadata.csv")
   features <- file.path(data.dir, "all_genes.csv")
   return(ReadMtx(