Version 5.5.1

Changes

Additions

• Added uwot.init parameter to RunUMAP to optionally customize method of UMAP initialization (#10386)

Fixes

• Fixed bug in PrepSCTFindMarkers in the multi-model case that produced zero counts for some valid genes due to an incorrect filter for theta (#10410)
• Fixed issue with FindClusters not setting metadata properly when a vector of resolutions is passed to resolution and a custom cluster name is specified (#10385)
• Updated logic in Parenting to extract function names from the call stack efficiently, avoiding slowdowns when functions are run with do.call (#10161)
• Fixed bug in PrepDR5 affecting RunPCA on v5 objects, where supplied features could be incorrectly dropped when non-supplied features had zero variance (#10398)
• Updated LabelClusters to use fill argument for label background color in geom_label* when specified, instead of the default per-cluster color (#10404)

Version 5.5.0

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)

Version 5.4.0

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)

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)

Version 5.3.0

Bug releases and performance improvements, including:

• Refactoring and speed-up of sctransform
• Refactroring and speed-up of leverage score calcluation
• Fixes to variable feature selection, module score calculation, PseudobulkExpression, and other bugs that could cause errors in edge cases
• Improved testing, CI

Version 5.2.1

Changes

• Fixed test_find_clusters.R to accommodate variability in label assignments given by FindClusters across different systems (#9641)

Version 5.2.0

Changes

• Added group.by parameter to FindAllMarkers, allowing users to regroup their data using a non-default identity class prior to performing differential expression (#9550)
• Added image.type parameter to Read10X_Image enabling VisiumV1 instances to be populated instead of instances of the default VisiumV2 class (#9556)
• Fixed IntegrateLayers to respect the dims.to.integrate parameter
• Added stroke.size parameter to DimPlot (#8180)
• Updated RunLeiden to use the leidenbase package instead of leiden; deprecated the method parameter for RunLeiden and FindClusters; updated RunLeiden to reset random.seed to 1 if the value is 0 or less (#6792)
• Updated RunPCA to use the BPCells-provided SVD solver on BPCells matrices; updated JackStraw to support BPCells matrices (#8271)
• Fixed RunPCA to avoid converting BPCells matrices into dense matrices - significantly reduces the function's memory usage when running on BPCells matrices (#8966)
• Updated RunSLSI to support BPCells matrices
• Fixed DietSeurat so that the layers parameter is respected (#8197)
• Updated RunUMAP to support umap-learn version >= 0.5.0 (#9559)
• Updated LoadXenium and ReadXenium to accommodate the output from XOA v3.0; updated LoadXenium to provide more fine-grained control over the datatypes parsed in, including nucleus segmentation masks, segmentation methods, and other experimental metadata; updated ReadXenium to load cell_feature_matrix.h5 when present in favor of the MEX format files; updated ReadXenium to load .parquet files using arrow instead of .csv.gz files to support XOA 3.0 (#8604)
• Fixed LoadXenium to accommodate datasets without "Blank Codeword" or "Unassigned Codeword" matrices(#9135)
• Fixed ReadXenium to properly parse multiple molecular outputs at once (#8265)
• Added features parameter to LeverageScore and SketchData
• Updated SketchData's ncells parameter to accept integer vector

Version 5.1.0

Changes

• Updated interactive SpatialDimPlots to display spatial coordinates
• Updated BuildClusterTree to PseudobulkExpression(..., method = "aggregate") instead of AverageExpression
• Fixed SpatialPlot to properly handle images with shared cells
• Added cluster.name parameter to BuildNicheAssay
• Added VisiumV2 class, inherits SeuratObject::FOV, returned by Load10X_Spatial
• Updated Load10X_Spatial to support loading Visium HD datasets - added bin.size parameter
• Updated Read10X_Coordinates to handle new tissue_coordinates.parquet files
• Added shape parameter to SpatialPlot and wrappers: SpatialFeaturePlot and SpatialDimPlot
• Added image.scale parameter to SpatialPlot and related functions: SpatialFeaturePlot/ISpatialFeaturePlot and SpatialDimPlot/ISpatialDimPlot
• Restored image.name parameter to Read10X_Image
• Added scale parameter to Radius.VisiumV1
• Fixed calculation of spot.radius attribute for VisiumV1 instance returned by Read10X_Image — replace scale.factors$fiducial with scale.factors$spot
• Added Read10X_Coordinates and Read10X_ScaleFactors
• Fixed SpatialPlot to properly handle mutli-assay Seurat instances

Version 5.0.3

Changes

• Fixed PercentAbove to discount null values (#8412)
• Added log parameter to FeatureScatter
• Fixed handling of clip.range for SCTransform when ncells is less than the size of the passed dataset

Version 5.0.2

Changes

• Fixed AverageExpression to handle features vector when layer="scale.data" and return.seurat=TRUE
• Added fc.slot parameter to FindMarkers
• Fixed SCTransform to handle vars.to.regress (#8148) and (#8349)
• Fixed SCTransform to handle fetching residuals (#8185)