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