Merge branch 'develop' into dimplot_stroke

.Rbuildignore

@@ -4,11 +4,8 @@
 ^\.Rproj\.user$
 ^.*\.old$
 .git
-.travis.yml
 appveyor.yml
-azure-pipelines.yml
 cran-comments.md
-travis_setup.sh
 CODE_OF_CONDUCT.md
 ^_pkgdown\.yaml$
 ^docs$

.github/workflows/integration_checks.yaml

@@ -0,0 +1,50 @@
+name: Integration Checks
+
+# Because `develop` is a protected branch this workflow is triggered when a PR 
+# is opened/updated and again when it is merged.
+on:
+  push:
+    branches: 
+    - develop
+  pull_request:
+    branches: 
+    - develop
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+
+    # Use the `satijalab/seurat-ci` Docker image as the runner environment. 
+    # This image is pre-configured with everything required for running
+    # integration checks, for more details, see
+    # https://hub.docker.com/repository/docker/satijalab/seurat-ci/general.
+    container:
+      image: satijalab/seurat-ci:latest
+
+    steps:
+      # Pull the latest changes from the repository down to the runner.
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      # Install the package and all its dependencies using scripts from 
+      # `littler`, see https://eddelbuettel.github.io/littler/ for details. 
+      - name: Install Dependencies
+        run: installDeps.r -s
+
+      # Run CRAN checks, if any ERRORs or WARNINGs are raised the check fails.
+      # Certain tests are skipped when running as CRAN—skip all tests so they
+      # can be run together in a subsequent step.
+      - name: Run CRAN Checks (no tests)
+        run: |
+          rcmdcheck::rcmdcheck(
+            args = c("--as-cran", "--no-tests"), 
+            error_on="warning"
+          )
+        shell: Rscript {0}
+
+      # Because tests weren't included in CRAN checks, run them here.
+      - name: Run Tests
+        # Run this step even if the previous one failed.
+        if: always()
+        run: testthat::test_local()
+        shell: Rscript {0}

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: Seurat
-Version: 5.0.1
-Date: 2023-11-16
+Version: 5.1.0.9012
 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 = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
   person(given = "Saket", family = "Choudhary", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = 'David', family = 'Collins', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-9243-7821')),
   person(given = "Charlotte", family = "Darby", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
   person(given = "Jeff", family = "Farrell", email = "[email protected]", role = "ctb"),
   person(given = "Isabella", family = "Grabski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-0616-5469")),
@@ -28,13 +28,14 @@ Authors@R: c(
   person(given = "Shiwei", family = "Zheng", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-6682-6743")),
   person("Satija Lab and Collaborators", role = "fnd")
   )
+License: MIT + file LICENSE
 URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
 Additional_repositories: https://satijalab.r-universe.dev, https://bnprks.r-universe.dev
 Depends:
     R (>= 4.0.0),
     methods,
-    SeuratObject (>= 5.0.0)
+    SeuratObject (>= 5.0.2)
 Imports:
     cluster,
     cowplot,
@@ -89,9 +90,44 @@ Imports:
     tools,
     utils,
     uwot (>= 0.1.10)
+Suggests:
+    ape,
+    arrow,
+    Biobase,
+    BiocGenerics,
+    BPCells,
+    data.table,
+    DESeq2,
+    DelayedArray,
+    enrichR,
+    GenomicRanges,
+    GenomeInfoDb,
+    glmGamPoi,
+    ggrastr,
+    harmony,
+    hdf5r,
+    IRanges,
+    limma,
+    MAST,
+    metap,
+    mixtools,
+    monocle,
+    presto,
+    rsvd,
+    R.utils,
+    Rfast2,
+    rtracklayer,
+    S4Vectors,
+    sf (>= 1.0.0),
+    SingleCellExperiment,
+    SummarizedExperiment,
+    testthat,
+    VGAM
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
-License: MIT + file LICENSE
+BuildManual: true
+Encoding: UTF-8
 LazyData: true
+RoxygenNote: 7.3.2
 Collate:
     'RcppExports.R'
     'reexports.R'
@@ -113,35 +149,3 @@ Collate:
     'sketching.R'
     'tree.R'
     'utilities.R'
-RoxygenNote: 7.2.3
-Encoding: UTF-8
-Suggests:
-    ape,
-    BPCells,
-    rsvd,
-    testthat,
-    hdf5r,
-    S4Vectors,
-    SummarizedExperiment,
-    SingleCellExperiment,
-    MAST,
-    DESeq2,
-    BiocGenerics,
-    GenomicRanges,
-    GenomeInfoDb,
-    IRanges,
-    rtracklayer,
-    Rfast2,
-    monocle,
-    Biobase,
-    VGAM,
-    limma,
-    metap,
-    enrichR,
-    mixtools,
-    ggrastr,
-    data.table,
-    R.utils,
-    presto,
-    DelayedArray,
-    harmony

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)
@@ -106,6 +107,7 @@ S3method(RunPCA,StdAssay)
 S3method(RunPCA,default)
 S3method(RunSLSI,Assay)
 S3method(RunSLSI,Seurat)
+S3method(RunSLSI,StdAssay)
 S3method(RunSLSI,default)
 S3method(RunSPCA,Assay)
 S3method(RunSPCA,Assay5)
@@ -133,6 +135,7 @@ 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 +156,7 @@ 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 +357,9 @@ 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 +469,11 @@ 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)
@@ -539,6 +547,7 @@ importFrom(SeuratObject,CreateAssayObject)
 importFrom(SeuratObject,CreateCentroids)
 importFrom(SeuratObject,CreateDimReducObject)
 importFrom(SeuratObject,CreateFOV)
+importFrom(SeuratObject,CreateMolecules)
 importFrom(SeuratObject,CreateSegmentation)
 importFrom(SeuratObject,CreateSeuratObject)
 importFrom(SeuratObject,DefaultAssay)

NEWS.md

@@ -1,3 +1,56 @@
+# Unreleased
+
+## Changes
+- Updated `RunUMAP` to support `umap-learn` version >= 0.5.0 ([#9559](https://github.com/satijalab/seurat/pull/9559))
+- Surfaced more fine-grained control over what parts of a Xenium experiment are loaded in `LoadXenium`
+- Added ability to load Xenium nucleus segmentation masks
+- Updated `LoadXenium` to also read some run metadata (run start time, preservation method, panel used, organism, tissue type, instrument software version and stain kit used) into `misc` slot
+- Updated `ReadXenium` to load cell_feature_matrix.h5 when present in favor of the MEX format files
+- Added ability to read Xenium `segmentation_method` directly into `meta.data`
+- Updated `ReadXenium` to load .parquet files using `arrow` instead of .csv.gz files to support XOA 3.0
+- Updated `RunSLSI` to support `BPCells` matrices
+- Fixed `LoadXenium` to accommodate datasets without "Blank Codeword" or "Unassigned Codeword" matrices
+- Fixed `ReadXenium` to properly parse multiple molecular outputs at once ([#8265](https://github.com/satijalab/seurat/issues/8265))
+- Fixed `RunPCA` to avoid converting `BPCells` matrices into dense matrices - significantly reduces the function's memory usage when running on `BPCells` matrices
+- Added `features` parameter to `LeverageScore` and `SketchData`
+- Updated `SketchData`'s `ncells` parameter to accept integer vector
+- Updated `JackStraw` to support `BPCells` matrices
+- Updated `RunPCA` to use the `BPCells`-provided SVD solver on `BPCells` matrices
+
+# 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
+- Fixed `PercentAbove` to discount null values ([#8412](https://github.com/satijalab/seurat/issues/8412))
+- Added `log` parameter to `FeatureScatter`
+- Fixed handling of `clip.range` for `SCTransform` when `ncells` is less than the size of the passed dataset
+
+# Seurat 5.0.2 (2024-02-28) 
+
+## Changes
+
+- Fixed `AverageExpression` to handle `features` vector when `layer="scale.data"` and `return.seurat=TRUE`
+- Added `fc.slot` parameter to `FindMarkers`
+- Fixed `SCTransform` to handle `vars.to.regress` ([#8148](https://github.com/satijalab/seurat/issues/8148)) and ([#8349](https://github.com/satijalab/seurat/issues/8349))
+- Fixed `SCTransform` to handle fetching residuals ([#8185](https://github.com/satijalab/seurat/issues/8185))
+
 # Seurat 5.0.1 (2023-11-16)
 
 ## Changes
@@ -188,6 +241,7 @@
 - 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