Changes
- Updated interactive
SpatialDimPlots to display spatial coordinates - Updated
BuildClusterTreetoPseudobulkExpression(..., method = "aggregate")instead ofAverageExpression - Fixed
SpatialPlotto properly handle images with shared cells - Added
cluster.nameparameter toBuildNicheAssay - Added
VisiumV2class, inheritsSeuratObject::FOV, returned byLoad10X_Spatial - Updated
Load10X_Spatialto support loading Visium HD datasets - addedbin.sizeparameter - Updated
Read10X_Coordinatesto handle newtissue_coordinates.parquetfiles - Added
shapeparameter toSpatialPlotand wrappers:SpatialFeaturePlotandSpatialDimPlot - Added
image.scaleparameter toSpatialPlotand related functions:SpatialFeaturePlot/ISpatialFeaturePlotandSpatialDimPlot/ISpatialDimPlot - Restored
image.nameparameter toRead10X_Image - Added
scaleparameter toRadius.VisiumV1 - Fixed calculation of
spot.radiusattribute forVisiumV1instance returned byRead10X_Image— replacescale.factors$fiducialwithscale.factors$spot - Added
Read10X_CoordinatesandRead10X_ScaleFactors - Fixed
SpatialPlotto properly handle mutli-assaySeuratinstances