Changelog • SeuratObject

Changes:

Add sf.data slot to the Segmentation class to store an sf object (#258)
- sf.data will represent segmentation boundaries for a given image inside the images slot of a Seurat object
- Add CreateSegmentation.sf, [[<-, setValidity for interacting with Segmentation objects
- Update RenameCells.Segmentation, subset.Segmentation, [, UpdateSeuratObject
Add optional misc slot to SpatialImage to store additional info associated with an object in a list (#258)

Changes:

Update subset.Seurat to call droplevels on the input’s cell-level meta.data slot; update subset.Assay to call droplevels on the input’s feature-level meta.features slot; update subset.StdAssay to call droplevels on the input’s feature-level meta.data slot (#251)
Update UpdateSeuratObject to call droplevels on the input’s cell-level meta.data slot (@samuel-marsh, #247)
Drop Seurat from Enhances; update .IsFutureSeurat to avoid calling requireNamespace('Seurat', ...) (#250)
Update the VariableFeatures.StdAssay setter to apply a speedup (#240)
Add SVFInfo.Assay5 & SpatiallyVariableFeatures.Assay5 (#242)
Fix bug in UpdateSeuratObject (@neanderthalensis, #210)
Fix bug in WhichCells.Seurat (@maxim-h, #219)
Fix bug in SpatiallyVariableFeatures.Assay (#242)
Fix bug in merge.Seurat (#246)
Fix bug in VariableFeatures.StdAssay (#245)
Fix bug in HVFInfo.StdAssay (#244)
Fix bug in RenameCells.Seurat (#237)
Fix bug in subset.StdAssay (#214)

Changes:

Properly re-export %||% from rlang (#178)
Class key-based warnings (#180)
Require R 4.1 (#180)
Fix errors in UpdateSeuratObject (@ddiez, #182)
Add ... to call signature for Radius generic (#190)
Fix bug in PolyVtx (#194)
Fix bug in feature-level subsetting (#200)
Update UpdateSeuratObject to run without Seurat installed (#199)
Add warning in Layers.Assay() when the search returns no results (@maxim-h, #189)
Fix bug in subset to allow empty images to be dropped (#204)

Changes:

Update internal calls to GetAssayData() to use layer instead of slot (#160)
Update Matrix version to 1.6-2 (#164)
Change layer-saving in SaveSeuratRds() to move all layers instead of just those in tempdir() (#169)
Update internal calls to SetAssayData() to use layer instead of slot (#171)
Replace internal calls of FilterObjects() to .FilterObjects() (#171)

Added

New Assay5 class with support for layers; layers provide support for:
- arbitrary expression matrix names and number
- arbitrary expression matrix shape
- disk-backed expression matrices
New $ method for Assay and Assay5 objects to pull expression matrices, replacing informal usage of @
New LayerData() and LayerData()<- functions to replace GetAssayData() and SetAssayData(), respectively
Support for renaming cells and features with dimnames()<- (changing feature names does not apply to v3 Assay objects)
New SaveSeuratRds() and LoadSeuratRds() to save and load Seurat objects with disk-backed layers
New droplevels.LogMap() to drop unused entries from a LogMap
New ability to split (split()) and rejoin layers (JoinLayers()) within Assay and Assay5 objects based on grouping factor

Changes

slot argument deprecated in all contexts; where applicable, replaced with layer argument
[ for Assay and Assay5 objects take a layer name to pull an expression matrix
- option Seurat.object.assay.brackets allows restoring v3/v4 behavior of subsetting the main expression matrix (eg. data)
Stricter object validation routines at all levels
PackageCheck() deprecated in favor of rlang::check_installed()
AttachDeps() deprecated in favor of using the Depends field of DESCRIPTION
Subobjects within a Seurat object may have subsets of cells present at the object level
Begun replacement of stop() and warning() with rlang::abort() and rlang::warn() for easier debugging
Expanded validation and utility of KeyMixin objects

Removed

Unused object constructors (eg. Assay(), Seurat())

Changes

Fixes for CellsByIdentities (#80)
Remove {rgeos} from Suggests and replace with {sf} due to {rgeos} package retirement
New check for potential binary breaks between dependencies and SeuratObject

Changes

Move {rgeos} to Suggests; segmentation simplification now requires {rgeos} to be installed manually
Move {sp} to Depends

Added

Add keys to Assays and DimReducs in UpdateSeuratObject when missing

Changed

Bump required Matrix version to >= 1.5.0

Changed

Update sparse matrix coersions due to Matrix deprecations

Changed

Allow UpdateSeuratObject to work when data is NULL (#38)
Fix superclass issue with R-devel 4.3.x (#42)

Added

New FOV, Segmentations, Centroids, and Molecules classes for imaging-based spatial datasets

Changed

CreateSeuratObject.Assay sets Assay key when not present (#29)
Ignore warnings when creating an Assay from a data frame (#32)

Added

New CheckMatrix generic for validating expression matrices

Changed

Export utility functions (#22)
Bug fix in names with Key.Seurat (#26)
Improved duplicate key checking and resolution

Changed

Provide default option for Seurat.checkdots option if option is not set (#16)

Added

head and tail methods for Seurat and Assay objects (#5)
New utility functions (#6):
- AttachDeps to attach required imported dependencies on package attachment
- IsMatrixEmpty to test if a matrix is empty or not

Changed

Allow super classes to replace child classes (#1). For example, allows Assay objects to replace Seurat::SCTAssay or Signac::ChromatinAssay objects of the same name
Better support for creating sparse matrices from data.table/tibble objects (#4)
Improved error messages for clashing object names (#7)
Allow returning a NULL if a subset results in zero cells (#9)

Removed

SCT-specific code (#2)

Initial release of SeuratObject