Merge pull request #8878 from satijalab/develop

Release/5.1.0

DESCRIPTION

@@ -1,11 +1,12 @@
 Package: Seurat
-Version: 5.0.3
-Date: 2024-03-18
+Version: 5.1.0
+Date: 2024-05-08
 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(
   person(given = "Andrew", family = "Butler", email = "abutler@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
   person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = 'David', family = 'Collins', email = 'dcollins@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9243-7821')),
   person(given = "Charlotte", family = "Darby", email = "cdarby@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
   person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"),
   person(given = "Isabella", family = "Grabski", email = "igrabski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-0616-5469")),
@@ -34,7 +35,7 @@ Additional_repositories: https://satijalab.r-universe.dev, https://bnprks.r-univ
 Depends:
     R (>= 4.0.0),
     methods,
-    SeuratObject (>= 5.0.0)
+    SeuratObject (>= 5.0.2)
 Imports:
     cluster,
     cowplot,
@@ -117,6 +118,7 @@ RoxygenNote: 7.3.1
 Encoding: UTF-8
 Suggests:
     ape,
+    arrow,
     BPCells,
     rsvd,
     testthat,

NAMESPACE

@@ -52,6 +52,7 @@ S3method(GetImage,VisiumV1)
 S3method(GetTissueCoordinates,STARmap)
 S3method(GetTissueCoordinates,SlideSeq)
 S3method(GetTissueCoordinates,VisiumV1)
+S3method(GetTissueCoordinates,VisiumV2)
 S3method(HVFInfo,SCTAssay)
 S3method(IntegrateEmbeddings,IntegrationAnchorSet)
 S3method(IntegrateEmbeddings,TransferAnchorSet)
@@ -133,6 +134,7 @@ S3method(ScaleData,Seurat)
 S3method(ScaleData,StdAssay)
 S3method(ScaleData,default)
 S3method(ScaleFactors,VisiumV1)
+S3method(ScaleFactors,VisiumV2)
 S3method(ScoreJackStraw,DimReduc)
 S3method(ScoreJackStraw,JackStrawData)
 S3method(ScoreJackStraw,Seurat)
@@ -153,6 +155,7 @@ S3method(components,SCTAssay)
 S3method(dim,STARmap)
 S3method(dim,SlideSeq)
 S3method(dim,VisiumV1)
+S3method(dim,VisiumV2)
 S3method(fortify,Centroids)
 S3method(fortify,Molecules)
 S3method(fortify,Segmentation)
@@ -353,7 +356,9 @@ export(PurpleAndYellow)
 export(RPCAIntegration)
 export(Radius)
 export(Read10X)
+export(Read10X_Coordinates)
 export(Read10X_Image)
+export(Read10X_ScaleFactors)
 export(Read10X_h5)
 export(Read10X_probe_metadata)
 export(ReadAkoya)
@@ -463,9 +468,11 @@ exportClasses(SeuratCommand)
 exportClasses(SpatialImage)
 exportClasses(TransferAnchorSet)
 exportClasses(VisiumV1)
+exportClasses(VisiumV2)
 importClassesFrom(Matrix,dgCMatrix)
 importClassesFrom(SeuratObject,Assay)
 importClassesFrom(SeuratObject,DimReduc)
+importClassesFrom(SeuratObject,FOV)
 importClassesFrom(SeuratObject,Graph)
 importClassesFrom(SeuratObject,JackStrawData)
 importClassesFrom(SeuratObject,Neighbor)

NEWS.md

@@ -1,3 +1,21 @@
+# Seurat 5.1.0 (2024-05-08)
+
+## Changes
+- Updated interactive `SpatialDimPlot`s to display spatial coordinates
+- Updated `BuildClusterTree` to `PseudobulkExpression(..., method = "aggregate")` instead of `AverageExpression`
+- Fixed `SpatialPlot` to properly handle images with shared cells
+- Added `cluster.name` parameter to `BuildNicheAssay`
+- Added `VisiumV2` class, inherits `SeuratObject::FOV`, returned by `Load10X_Spatial`
+- Updated `Load10X_Spatial` to support loading Visium HD datasets - added `bin.size` parameter 
+- Updated `Read10X_Coordinates` to handle new `tissue_coordinates.parquet` files
+- Added `shape` parameter to `SpatialPlot` and wrappers: `SpatialFeaturePlot` and `SpatialDimPlot`
+- Added `image.scale` parameter to `SpatialPlot` and related functions: `SpatialFeaturePlot`/`ISpatialFeaturePlot` and `SpatialDimPlot`/`ISpatialDimPlot`
+- Restored `image.name` parameter to `Read10X_Image`
+- Added `scale` parameter to `Radius.VisiumV1`
+- Fixed calculation of `spot.radius` attribute for `VisiumV1` instance returned by `Read10X_Image` — replace `scale.factors$fiducial` with `scale.factors$spot`
+- Added `Read10X_Coordinates` and `Read10X_ScaleFactors`
+- Fixed `SpatialPlot` to properly handle mutli-assay `Seurat` instances
+
 # Seurat 5.0.3 (2024-03-18)
 
 ## Changes

R/convenience.R

@@ -258,7 +258,9 @@ SpatialDimPlot <- function(
   pt.size.factor = 1.6,
   alpha = c(1, 1),
   image.alpha = 1,
-  stroke = 0.25,
+  image.scale = "lowres",
+  shape = 21,
+  stroke = NA,
   label.box = TRUE,
   interactive = FALSE,
   information = NULL
@@ -281,6 +283,8 @@ SpatialDimPlot <- function(
     pt.size.factor = pt.size.factor,
     alpha = alpha,
     image.alpha = image.alpha,
+    image.scale = image.scale,
+    shape = shape,
     stroke = stroke,
     label.box = label.box,
     interactive = interactive,
@@ -307,7 +311,9 @@ SpatialFeaturePlot <- function(
   pt.size.factor = 1.6,
   alpha = c(1, 1),
   image.alpha = 1,
-  stroke = 0.25,
+  image.scale = "lowres",
+  shape = 21,
+  stroke = NA,
   interactive = FALSE,
   information = NULL
 ) {
@@ -325,6 +331,8 @@ SpatialFeaturePlot <- function(
     pt.size.factor = pt.size.factor,
     alpha = alpha,
     image.alpha = image.alpha,
+    image.scale = image.scale,
+    shape = shape,
     stroke = stroke,
     interactive = interactive,
     information = information

R/differential_expression.R

@@ -910,9 +910,9 @@ FindMarkers.DimReduc <- function(
 #'
 FindMarkers.Seurat <- function(
   object,
-  latent.vars = NULL,
   ident.1 = NULL,
   ident.2 = NULL,
+  latent.vars = NULL,
   group.by = NULL,
   subset.ident = NULL,
   assay = NULL,

R/generics.R

@@ -321,7 +321,6 @@ IntegrateEmbeddings <- function(anchorset, ...) {
 #'
 #' @export
 #'
-#'
 LeverageScore <- function(object, ...) {
   UseMethod(generic = 'LeverageScore', object = object)
 }
@@ -454,6 +453,7 @@ ProjectUMAP <- function(query, ...) {
 #'
 #' @rdname PseudobulkExpression
 #' @export PseudobulkExpression
+#' @concept utilities
 #'
 PseudobulkExpression <- function(object, ...) {
   UseMethod(generic = "PseudobulkExpression", object = object)

R/integration.R

@@ -981,7 +981,7 @@ FindTransferAnchors <- function(
       LayerData(object = combined.ob, layer = data.layer.name) <- layer.data # set layer data
     }
     colnames(x = orig.loadings) <- paste0("ProjectPC_", 1:ncol(x = orig.loadings))
-    
+
     combined.ob[["pcaproject"]] <- combined.pca
     Loadings(object = combined.ob[["pcaproject"]], projected = FALSE) <- orig.loadings[, dims]
     Loadings(object = combined.ob[["pcaproject"]]) <- orig.loadings[, dims]
@@ -1901,6 +1901,7 @@ IntegrateEmbeddings.TransferAnchorSet <- function(
 #' @importFrom Matrix t
 #'
 #' @export
+#' @concept integration
 #'
 ProjectIntegration <- function(
   object,
@@ -3056,6 +3057,7 @@ SelectIntegrationFeatures <- function(
 #' @param ... Arguments passed on to \code{method}
 #'
 #' @export
+#' @concept integration
 #'
 SelectIntegrationFeatures5 <- function(
   object,
@@ -3088,6 +3090,7 @@ SelectIntegrationFeatures5 <- function(
 #' @param ... Arguments passed on to \code{method}
 #'
 #' @export
+#' @concept integration
 #'
 SelectSCTIntegrationFeatures <- function(
   object,
@@ -6506,6 +6509,7 @@ ValidateParams_IntegrateEmbeddings_TransferAnchors <- function(
 #' @importFrom Matrix sparseMatrix
 #'
 #' @export
+#' @concept integration
 #'
 NNtoGraph <- function(
   nn.object,
@@ -6670,7 +6674,9 @@ FindAssayAnchor <- function(
 #'
 #' @importFrom MASS ginv
 #' @return Returns a object list in which each object has a bridge cell derived assay
+#'
 #' @export
+#' @concept integration
 #'
 BridgeCellsRepresentation <- function(object.list,
                                       bridge.object,
@@ -6822,7 +6828,8 @@ BridgeCellsRepresentation <- function(object.list,
 #' @return Returns an \code{\link{AnchorSet}} object that can be used as input to
 #' \code{\link{IntegrateEmbeddings}}.or \code{\link{MapQuery}}
 #'
-
+#' @keywords internal
+#'
 FindBridgeAnchor <- function(object.list,
                              bridge.object,
                              object.reduction,
@@ -7346,7 +7353,10 @@ SmoothLabels <- function(labels, clusters) {
 #' @param verbose Print progress and message
 #'
 #' @return Returns a query-only or query-reference combined seurat object
+#'
 #' @export
+#' @concept integration
+#'
 ProjectDimReduc <- function(query,
                             reference,
                             mode = c('pcaproject', 'lsiproject'),
@@ -7492,11 +7502,13 @@ ProjectDimReduc <- function(query,
 #' @param laplacian.reduction.dims Number of dimensions used for graph laplacian eigenspace (default is 50)
 #' @param verbose Print progress and message (default is TRUE)
 #'
-#' @export
 #' @return Returns a \code{BridgeReferenceSet} that can be used as input to
 #'  \code{\link{FindBridgeTransferAnchors}}.
 #' The parameters used are stored in the \code{BridgeReferenceSet} as well
 #'
+#' @export
+#' @concept integration
+#'
 PrepareBridgeReference <- function (
   reference,
   bridge,
@@ -7642,11 +7654,13 @@ PrepareBridgeReference <- function (
 #' }
 #' @param verbose Print messages and progress
 #'
-#' @export
 #' @return Returns an \code{AnchorSet} object that can be used as input to
 #' \code{\link{TransferData}}, \code{\link{IntegrateEmbeddings}} and
 #' \code{\link{MapQuery}}.
 #'
+#' @export
+#' @concept integration
+#'
 FindBridgeTransferAnchors <- function(
   extended.reference,
   query,
@@ -7725,10 +7739,12 @@ FindBridgeTransferAnchors <- function(
 #' }
 #' }
 #'
-#' @export
 #' @return Returns an \code{AnchorSet} object that can be used as input to
 #' \code{\link{IntegrateEmbeddings}}.
 #'
+#' @export
+#' @concept integration
+#'
 FindBridgeIntegrationAnchors <- function(
   extended.reference,
   query,
@@ -7807,6 +7823,7 @@ FindBridgeIntegrationAnchors <- function(
 #' @importFrom rlang exec
 #' @return Returns a Seurat object with integrated dimensional reduction
 #' @export
+#' @concept integration
 #'
 FastRPCAIntegration <- function(
   object.list,
@@ -7912,6 +7929,7 @@ FastRPCAIntegration <- function(
 #' @importFrom Matrix t
 #'
 #' @export
+#' @concept integration
 #'
 UnSketchEmbeddings <- function(
   atom.data,

R/integration5.R

@@ -158,6 +158,7 @@ attr(x = HarmonyIntegration, which = 'Seurat.method') <- 'integration'
 #'
 #' @inheritParams RPCAIntegration
 #' @export
+#' @concept integration
 #'
 #' @examples
 #' \dontrun{
@@ -342,6 +343,8 @@ attr(x = CCAIntegration, which = 'Seurat.method') <- 'integration'
 #' @param ... Arguments passed on to \code{FindIntegrationAnchors}
 #' @export
 #'
+#' @concept utilities
+#'
 RPCAIntegration <- function(
     object = NULL,
     assay = NULL,
@@ -444,6 +447,7 @@ attr(x = RPCAIntegration, which = 'Seurat.method') <- 'integration'
 #' @inheritParams IntegrateEmbeddings
 #' @param ... Arguments passed on to \code{FindIntegrationAnchors}
 #' @export
+#' @concept integration
 #'
 JointPCAIntegration <- function(
     object = NULL,