SeuratObject 5.3.0

Changes:

• Update subset.Seurat to no longer call droplevels on the input's cell-level meta.data slot; update subset.Assay to no longer call droplevels on the input's feature-level meta.features slot; update subset.StdAssay to no longer call droplevels on the input's feature-level meta.data slot (reverting #251, see discussion in #247)
• Add drop = FALSE when retrieving data in LayerData.Assay to preserve dimensions when subsetting to the requested cells (#261)
• Update sf.data slot in the Segmentation class to store a data.frame in accordance with changes in loading Visium segmentations (#267)
• Add compact slot to the Segmentation class to denote whether the object only stores segmentation information in the sf.data slot, or also the sp-inherited slots (#267)
• Update CreateSegmentation, CreateSegmentation.data.frame, CreateSegmentation.sf, and methods interacting with Segmentation objects (Cells.Segmentation, RenameCells.Segmentation, Crop.Segmentation, subset.Segmentation, [[<-, coordinates, Overlay, show, setValidity) to account for the addition of compact and the update to sf.data
  • For a detailed description of changes, see #267
• Add coords_x_orientation slot to the FOV class to hold the orientation of the x-axis for spatial data (to mark whether the coordinate system of a spatial object has been updated)
• Update UpdateSeuratObject to check whether an object requires an update to the coordinate system based on the existence and value of the coords_x_orientation slot (currently only relevant for Visium objects)
• Add method safeValidityCheck to show an improved error message suggesting to run UpdateSeuratObject when a "slots in class definition but not in object" error is thrown by R's internal object validation; use in FOV-interacting methods

SeuratObject 5.2.0

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)

SeuratObject 5.1.0

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)

SeuratObject 5.0.2

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)

SeuratObject 5.0.1

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)

SeuratObject 5.0.0

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())

SeuratObject 4.1.4

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

SeuratObject 4.1.3

Changes

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

Added

• Add keys to Assays and DimReducs in UpdateSeuratObject when missing

SeuratObject 4.1.0

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

SeuratObject 4.0.4

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