Changes

Additions

• Added support for 10x Space Ranger 4.0 outputs (Visium data with segmentations)
  • Updated data loading functions Load10X_Spatial, Read10X_Image
  • Updated GetTissueCoordinates.VisiumV2
  • Updated spatial visualization functions SpatialPlot, SingleSpatialPlot, SpatialDimPlot, SpatialFeaturePlot
  • Added helper functions Read10X_Segmentations, Read10X_HD_GeoJson, Format10X_GeoJson_CellID
• Added function InteractiveSpatialPlot to allow users to interactively lasso-select cells from a spatial Seurat object (Visium, SlideSeq, or Vizgen data)

Fixes

• Updated loading & visualization functions (see above for list) for Visium objects -- see #10125 for details
  • For binned Visium data, x now correctly corresponds to imagecol from tissue positions; y now correctly corresponds to imagerow from tissue positions; these are now consistent with 10X's coordinate system (with the origin being the top left).
• Reverted #10062 in favor of fetching both grouping variables and dimensionality reduction embeddings with FetchData as previously; added warning to alert users when column names of metadata and dimensionality reduction embeddings conflict
• Added color retrieval logic in LabelClusters for consistent cluster label coloring (#10198)