satijalab/seurat v3.2.1

Version 3.2.1

on GitHub

Deprecations

• CreateActivityMatrix deprecated in favor of Signac::GeneActivity
• ReadAlevin and ReadAlevinCsv deprecated in favor of SeuratWrappers::ReadAlevin
• ExportToCellbrowser and StopCellbrowser deprecated in favor of SeuratWrappers::ExportToCellbrowser and SeuratWrappers::StopCellbrowser
• ReadH5AD and WriteH5AD deprecated in favor of h5Seurat/H5AD functionality found in SeuratDisk
• as.loom and as.Seurat.loom deprecated in favor of functionality found in SeuratDisk

Changes

• Allow setting slot parameter in RunUMAP
• Added support for FIt-SNE v1.2+
• Fix for Spatial*Plot when running with interactive=TRUE
• Set max for number of items returned by Top and remove duplicate items when balanced=TRUE
• Fix logging bug when functions were run via do.call()
• Fix handling of weight.by.var parameter when approx=FALSE in RunPCA()
• Fix issue where feature names with dashes crashed CellSelector
• Fix issue where errors in subsetting were being swallowed
• Fix issue where labeling uncropped spatial plots was broken

Additions

• Added support for nearest neighbor input and return.model parameter in RunUMAP()
• Enable named color vectors in DoHeatmap()
• Add label.color and label.box parameters to DimPlot
• Added shuffle and seed parameters to DimPlot() to help with overplotting
• Added new stacked violin plot functionality