Merge pull request #6758 from satijalab/release/4.3.0

Seurat v4.3.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.2.1
-Date: 2022-11-07
+Version: 4.3.0
+Date: 2022-11-18
 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(
@@ -10,8 +10,10 @@ 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 = "Austin", family = "Hartman", email = "ahartman@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
   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 = "Madeline", family = "Kowalski", email = "mkowalski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
   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"),
   person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833")),
@@ -55,6 +57,7 @@ Imports:
     pbapply,
     plotly (>= 4.9.0),
     png,
+    progressr,
     RANN,
     RColorBrewer,
     Rcpp (>= 1.0.7),
@@ -95,7 +98,7 @@ Collate:
     'tree.R'
     'utilities.R'
     'zzz.R'
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 Encoding: UTF-8
 Suggests:
     ape,
@@ -120,4 +123,6 @@ Suggests:
     metap,
     enrichR,
     mixtools,
-    ggrastr
+    ggrastr,
+    data.table,
+    R.utils

NAMESPACE

@@ -103,13 +103,18 @@ S3method(as.sparse,H5Group)
 S3method(dim,STARmap)
 S3method(dim,SlideSeq)
 S3method(dim,VisiumV1)
+S3method(fortify,Centroids)
+S3method(fortify,Molecules)
+S3method(fortify,Segmentation)
 S3method(levels,SCTAssay)
 S3method(merge,SCTAssay)
 S3method(subset,AnchorSet)
 S3method(subset,SCTAssay)
 S3method(subset,STARmap)
 S3method(subset,SlideSeq)
 S3method(subset,VisiumV1)
+export("%iff%")
+export("%||%")
 export("DefaultAssay<-")
 export("Idents<-")
 export("Index<-")
@@ -208,6 +213,8 @@ export(IFeaturePlot)
 export(ISpatialDimPlot)
 export(ISpatialFeaturePlot)
 export(Idents)
+export(ImageDimPlot)
+export(ImageFeaturePlot)
 export(Images)
 export(Index)
 export(Indices)
@@ -226,8 +233,13 @@ export(LabelPoints)
 export(LinkedDimPlot)
 export(LinkedFeaturePlot)
 export(Load10X_Spatial)
+export(LoadAkoya)
 export(LoadAnnoyIndex)
+export(LoadHuBMAPCODEX)
+export(LoadNanostring)
 export(LoadSTARmap)
+export(LoadVizgen)
+export(LoadXenium)
 export(Loadings)
 export(LocalStruct)
 export(LogNormalize)
@@ -270,10 +282,15 @@ export(Radius)
 export(Read10X)
 export(Read10X_Image)
 export(Read10X_h5)
+export(ReadAkoya)
 export(ReadMtx)
+export(ReadNanostring)
 export(ReadParseBio)
 export(ReadSTARsolo)
 export(ReadSlideSeq)
+export(ReadVitessce)
+export(ReadVizgen)
+export(ReadXenium)
 export(Reductions)
 export(RegroupIdents)
 export(RelativeCounts)
@@ -314,6 +331,7 @@ export(SingleCorPlot)
 export(SingleDimPlot)
 export(SingleExIPlot)
 export(SingleImageMap)
+export(SingleImagePlot)
 export(SingleRasterMap)
 export(SingleSpatialPlot)
 export(SpatialDimPlot)
@@ -396,6 +414,10 @@ importFrom(RcppAnnoy,AnnoyEuclidean)
 importFrom(RcppAnnoy,AnnoyHamming)
 importFrom(RcppAnnoy,AnnoyManhattan)
 importFrom(Rtsne,Rtsne)
+importFrom(SeuratObject,"%!NA%")
+importFrom(SeuratObject,"%NA%")
+importFrom(SeuratObject,"%iff%")
+importFrom(SeuratObject,"%||%")
 importFrom(SeuratObject,"DefaultAssay<-")
 importFrom(SeuratObject,"Idents<-")
 importFrom(SeuratObject,"Index<-")
@@ -408,16 +430,24 @@ importFrom(SeuratObject,"Tool<-")
 importFrom(SeuratObject,"VariableFeatures<-")
 importFrom(SeuratObject,AddMetaData)
 importFrom(SeuratObject,Assays)
+importFrom(SeuratObject,AttachDeps)
+importFrom(SeuratObject,Boundaries)
 importFrom(SeuratObject,Cells)
 importFrom(SeuratObject,CellsByIdentities)
 importFrom(SeuratObject,Command)
 importFrom(SeuratObject,CreateAssayObject)
+importFrom(SeuratObject,CreateCentroids)
 importFrom(SeuratObject,CreateDimReducObject)
+importFrom(SeuratObject,CreateFOV)
+importFrom(SeuratObject,CreateSegmentation)
 importFrom(SeuratObject,CreateSeuratObject)
 importFrom(SeuratObject,DefaultAssay)
+importFrom(SeuratObject,DefaultBoundary)
 importFrom(SeuratObject,DefaultDimReduc)
+importFrom(SeuratObject,DefaultFOV)
 importFrom(SeuratObject,Distances)
 importFrom(SeuratObject,Embeddings)
+importFrom(SeuratObject,Features)
 importFrom(SeuratObject,FetchData)
 importFrom(SeuratObject,GetAssayData)
 importFrom(SeuratObject,GetImage)
@@ -430,10 +460,13 @@ importFrom(SeuratObject,Indices)
 importFrom(SeuratObject,IsGlobal)
 importFrom(SeuratObject,JS)
 importFrom(SeuratObject,Key)
+importFrom(SeuratObject,Keys)
 importFrom(SeuratObject,Loadings)
 importFrom(SeuratObject,LogSeuratCommand)
 importFrom(SeuratObject,Misc)
+importFrom(SeuratObject,Molecules)
 importFrom(SeuratObject,Neighbors)
+importFrom(SeuratObject,Overlay)
 importFrom(SeuratObject,PackageCheck)
 importFrom(SeuratObject,Project)
 importFrom(SeuratObject,Radius)
@@ -485,6 +518,7 @@ importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,fortify)
 importFrom(ggplot2,geom_abline)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_blank)
@@ -519,6 +553,7 @@ importFrom(ggplot2,margin)
 importFrom(ggplot2,position_dodge)
 importFrom(ggplot2,position_jitterdodge)
 importFrom(ggplot2,scale_alpha)
+importFrom(ggplot2,scale_alpha_manual)
 importFrom(ggplot2,scale_alpha_ordinal)
 importFrom(ggplot2,scale_color_brewer)
 importFrom(ggplot2,scale_color_distiller)
@@ -597,6 +632,7 @@ importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,plot.igraph)
 importFrom(irlba,irlba)
 importFrom(jsonlite,fromJSON)
+importFrom(jsonlite,read_json)
 importFrom(leiden,leiden)
 importFrom(lmtest,lrtest)
 importFrom(matrixStats,rowAnyNAs)
@@ -606,11 +642,13 @@ importFrom(matrixStats,rowSums2)
 importFrom(methods,"slot<-")
 importFrom(methods,.hasSlot)
 importFrom(methods,as)
+importFrom(methods,getMethod)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,setAs)
 importFrom(methods,setClass)
 importFrom(methods,setClassUnion)
+importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,setOldClass)
 importFrom(methods,setValidity)
@@ -631,12 +669,15 @@ importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
 importFrom(plotly,raster2uri)
 importFrom(png,readPNG)
+importFrom(progressr,progressor)
 importFrom(reticulate,import)
 importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_seed)
 importFrom(rlang,"!!")
 importFrom(rlang,as_label)
 importFrom(rlang,invoke)
+importFrom(rlang,is_na)
+importFrom(rlang,sym)
 importFrom(scales,brewer_pal)
 importFrom(scales,hue_pal)
 importFrom(scales,rescale)
@@ -706,6 +747,7 @@ importFrom(stats,var)
 importFrom(stats,wilcox.test)
 importFrom(tibble,tibble)
 importFrom(tools,file_ext)
+importFrom(tools,file_path_sans_ext)
 importFrom(utils,argsAnywhere)
 importFrom(utils,capture.output)
 importFrom(utils,file_test)

NEWS.md

@@ -1,4 +1,12 @@
-# Seurat 4.2.1 (2022-11-07)
+# Seurat 4.3.0 (2022-11-18)
+
+## Added
+- Add support for imaging-based spatial datasets
+
+## Changes
+- Fix bug in `FindMarkers()` when run post Integration/Transfer ([#6856](https://github.com/satijalab/seurat/issues/6586))
+
+# Seurat 4.2.1 (2022-11-08)
 
 ## Changes
 - Replaced import from `spatstat.core` with `spatstat.explore`