NEWS.md
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)drop = FALSE when retrieving data in LayerData.Assay to preserve dimensions when subsetting to the requested cells (#261)sf.data slot in the Segmentation class to store a data.frame in accordance with changes in loading Visium segmentations (#267)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)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
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)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)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 methodssf.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 objectCreateSegmentation.sf, [[<-, setValidity for interacting with Segmentation objectsRenameCells.Segmentation, subset.Segmentation, [, UpdateSeuratObject
misc slot to SpatialImage to store additional info associated with an object in a list (#258)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)UpdateSeuratObject to call droplevels on the input’s cell-level meta.data slot (@samuel-marsh, #247)Seurat from Enhances; update .IsFutureSeurat to avoid calling requireNamespace('Seurat', ...) (#250)VariableFeatures.StdAssay setter to apply a speedup (#240)SVFInfo.Assay5 & SpatiallyVariableFeatures.Assay5 (#242)UpdateSeuratObject (@neanderthalensis, #210)WhichCells.Seurat (@maxim-h, #219)SpatiallyVariableFeatures.Assay (#242)merge.Seurat (#246)VariableFeatures.StdAssay (#245)HVFInfo.StdAssay (#244)RenameCells.Seurat (#237)subset.StdAssay (#214)%||% from rlang (#178)UpdateSeuratObject (@ddiez, #182)... to call signature for Radius generic (#190)PolyVtx (#194)UpdateSeuratObject to run without Seurat installed (#199)Layers.Assay() when the search returns no results (@maxim-h, #189)subset to allow empty images to be dropped (#204)GetAssayData() to use layer instead of slot (#160)SaveSeuratRds() to move all layers instead of just those in tempdir() (#169)SetAssayData() to use layer instead of slot (#171)FilterObjects() to .FilterObjects() (#171)Assay5 class with support for layers; layers provide support for:
$ method for Assay and Assay5 objects to pull expression matrices, replacing informal usage of @
LayerData() and LayerData()<- functions to replace GetAssayData() and SetAssayData(), respectivelydimnames()<- (changing feature names does not apply to v3 Assay objects)SaveSeuratRds() and LoadSeuratRds() to save and load Seurat objects with disk-backed layersdroplevels.LogMap() to drop unused entries from a LogMap
split()) and rejoin layers (JoinLayers()) within Assay and Assay5 objects based on grouping factorslot 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
Seurat.object.assay.brackets allows restoring v3/v4 behavior of subsetting the main expression matrix (eg. data)PackageCheck() deprecated in favor of rlang::check_installed()
AttachDeps() deprecated in favor of using the Depends field of DESCRIPTION
Seurat object may have subsets of cells present at the object levelstop() and warning() with rlang::abort() and rlang::warn() for easier debuggingKeyMixin objectsCellsByIdentities (#80)Seurat.checkdots option if option is not set (#16)Assay objects to replace Seurat::SCTAssay or Signac::ChromatinAssay objects of the same namedata.table/tibble objects (#4)NULL if a subset results in zero cells (#9)