Version 5.3.1

Changes

Additions

• Added option to use cluster_leiden from igraph when running Leiden clustering (#9931)
• Added option to use umap2 from uwot when running UMAP (#9918)
• Added option to use approx_pow parameter from uwot when running UMAP (#9449)
• Updated LoadXenium to add support for Xenium protein data (#10024)
• Added option to specify stroke size in FeaturePlot (#10053)
• Added label.size.cutoff parameter to DimPlot to allow users to label only clusters above a certain size (#10092)

Fixes

• Fixed deprecated calls to Seurat functions GetAssayData and PackageCheck (#9924), (#10102)
• Fixed errors in RunAzimuth relating to FindTransferAnchors (#9924)
• Fixed errors in LeverageScore relating to handling of (variable) features (#9924)
• Updated PseudobulkExpression to acccount for the case that a category passed to group.by has only one value (#10092)
• Updated VlnPlot to use assay passed to the function if specified (#10092)
• Updated FeatureScatter to allow gene names with parentheses to be plotted (#10092)
• Updated SingleRasterMap to store object metadata correctly (#10092)
• Updated FindClusters to order cluster factor levels correctly when assigning a custom cluster name (#10092)
• Updated FindConservedMarkers to remove NA values (#9917)
• Updated visualization functions to avoid ggplot2 guides, aes_string, and facet_grid deprecation warnings (#9409, #10116)
• Fixed DimPlot bug where metadata columns named 'PC_1', 'UMAP_1' etc override reduction embeddings (#10062)