Changes

Additions

• Added support for vars.to.regress and latent.data in ScaleData.IterableMatrix (BPCells) (#10300)
• Added warning to SCTransform to notify that do.correct.umi is hard set to F when a reference SCT model is specified (#10329, #10366)
• Added warning to FindMarkers/FindAllMarkers when running on an IterableMatrix (BPCells) with column-major storage order (#10365)
• Added plot_type parameter to ElbowPlot to switch between default (PCs x standard deviation) and two new options:
  • PCs x % variance explained (#8929)
  • PCs x cumulative % variance explained (#10369)
• Added legend.position parameter DimHeatmap to allow repositioning of legend when combine = T (#9813)
• Added "selected cells" indicator in InteractiveSpatialPlot (#10254)
• Added stroke.alpha parameter to SpatialPlot to be able to control transparency for fill and stroke separately (#10345)
• Added support for unnamed cols vectors in SpatialPlot (#10298)
• Added assay parameter to FeaturePlot to specify assay to pull features from (#10349)

Fixes

• Fixed issue with UMAP version parsing in RunUMAP (#10246)
• Updated HTODemux to handle HTO assays containing a subset of cells (#10362)
• Updated Rcpp error handling (#10317, #10353)
• Fixed issue with NaN values being propagated in PrepSCTFindMarkers (#10361)
• Fixed umi.assay labeling for model list in SCTransform to match the assay specified (#10330)
• Fixed factor-level ordering for metadata columns resulting from FindClusters (#10253)
• Fixed error in FindSpatiallyVariableFeatures from use of slot in function cascade (#10285)
• Fixed classification of gRNA with less than 5 cells in RunMixscape for proper label as "NP" (#10299)
• Fixed issue with checking object scope in as.Seurat.SingleCellExperiment (#10339)
• Fixed SketchData to pass the provided argument for verbose to LeverageScore (#10145)
• Fixed FindConservedMarkers to pass the provided argument for min.cells.group to FindMarkers (#8910)
• Updated IntegrateEmbeddings to respect dims.to.integrate when reference is specified (#10172)
• Fixed list structure of neighbors in FindNeighbors when SNN is not computed (#10364)
• Updated DimHeatmap to add PC labels as individual titles (#9813)
• Updated layer-building logic in Single/MultiExIPlot for ggplot2 v4+ compatibility (#10333)
• Fixed order = T in rasterized Dim/FeaturePlots via ggrastr-based rasterization (#10307, #10344)
• Updated SpatialPlot coordinate system check when plotting VisiumV1 images (#10267)
• Updated SpatialPlot for Visium data to speed up plot construction (#10345)
• Fixed interactive functionality of LinkedDim/LinkedFeaturePlot and interactive mode in SpatialPlot (#10368)
• Updated coordinate systems used for plot display in InteractiveSpatialPlot (#10254)
• Fixed coordinate ranges when spatial plots are generated with crop = F (#10278, #10284)