Version 4.0.1

Changes

• Equality added to differential expression thresholds in FindMarkers (e.g, >= logfc.threshold rather than >)
• Read10X() now prepends dataset number for first dataset when reading multiple datasets
• Bug fix for subset.AnchorSet()
• Bug fix for fold change values in FindMarkers() when setting a different pseudocount (#4111)
• Bug fix for RunLDA() related to proper passing of assay parameter.
• When using order=TRUE in SingleDimPlot(), print NA points under all others.
• Remove default parameter value for data.dir in Read10X()
• Import spatstat fxns from subpackages (spatstat.core, spatstat.geom)
• RunUMAP now checks for graph/neighbor consistency

Additions

• Add direction option to PlotClusterTree()
• Add cols parameter to JackStrawPlot()
• Add ReadMtx() to read local and remote mtx files with associated cell and feature name files

Version 4.0.0

Changes

• Removed old, deprecated code
• Utilize SeuratObject as base of object code
• Default neighbor finding algorithm changed from "rann" to "annoy"
• Default ncells parameter in SCTransform() changed to 5000
• Default fold change in FindMarkers() changed from ln to log2
• Implementation improvements to AverageExpression()
• AnchorSet class re-implemented as a virtual class from which IntegrationAnchorSet and TransferAnchorSet now inherit.
• Point size in VlnPlot() now set automatically if not specified
• Return the sample.tree properly when integrating with a single reference dataset
• Replace as.character.quosure usage with as_label due to deprecation
• Minor changes to the exact calculation of the anchor weight matrix
• Default rasterization limit in DimPlot() and FeaturePlot() changed from 50,000 to 100,000
• SCTransform() now returns a formalized Assay subclass SCTAssay()
• When using normalization.method='SCT' in FindTransferAnchors(), normalize query using reference SCT model when possible.

Additions

• Expose FoldChange() component in FindMarkers()
• Add IntegrateEmbeddings() to correct embeddings of DimReducs
• Add ProjectUMAP() to project query cells into a reference UMAP space
• Add MapQuery() as a wrapper around IntegrateData(), IntegrateEmbeddings(), and ProjectUMAP()
• Add MappingScore to compute a per-cell mapping score used in Azimuth
• Add AggregateExpression() for summation based pseudobulk calculations
• Add mixscape functionality via CalcPerturbSig(), PrepLDA(), RunLDA(), DEenrichRPlot(), MixscapeHeatmap(), MixscapeLDA(), PlotPerturbScore(), RunMixscape()
• Add FindSubCluster() to further cluster existing clusters
• Add supervised PCA functionality via RunSPCA()
• Add functionality to enable weighted nearest neighbor analyses via FindMultiModalNeighbors()
• Add neighbor visualization plot via NNPlot().
• Add PredictAssay() to impute expression or embeddings from nearest neighbors
• Add AnnotateAnchors() to aid in AnchorSet interpretation as well as subset.AnchorSet()
• Add flexibility of choice for cell column in Read10X()
• Add rasterization option to FeatureScatter() and VariableFeaturePlot()

Version 3.2.3

Deprecations

• do.cpp parameter in IntegrateData and TransferData deprecated and will default to true

Changes

• Same deprecated in favor of base::identity
• Fix in DietSeurat to work with specialized Assay objects
• Fix p-value return when using the ape implementation of Moran's I
• Fix bug in FindMarkers when using MAST with a latent variable
• Updates to Key<-.DimReduc that allow handling of empty reduction column names
• Allow setting ctrl in CellCycleScoring
• Modify subset.Seurat to allow specialized Assay subsetting methods
• Fix image selection in interactive spatial plots
• Update Rcpp functions with export(rng=FALSE) to avoid potential future warnings
• Fix RenameCells bug for integrated SCT assays
• Fix highlight order with proper factor levels when using SetHighlight in plots
• Small change in CellRanger version detection logic of h5 file to improve robustness to outside tools.

Additions

• Titles added to DimPlot when specifying group.by parameter
• keep.scale parameter added to FeaturePlot to control scaling across multiple features and/or splits.
• raster parameter in various scatter plots (eg. DimPlot, FeaturePlot, CellScatter) for plot-native rasterization instead of using AugmentPlot

Version 3.2.2

Changes

• Set the seed in WhichCells regardless of whether or not idents is passed
• Retain Graph and Neighbor objects when subsetting only on features
• Fix data.frame input to CreateAssayObject() when data.frame has no rownames.
• Default annoy search to sequential if not using multicore future plans.
• Require sctransform >= 0.3.0

Version 3.2.1

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

Version 3.2.0

Changes:

• Removed add.iter parameter from RunTSNE function
• Fixed integer overflow error in the WilcoxDETest function
• Minor visual fixes in DoHeatmap group bar + labels
• Efficiency improvements in anchor scoring (ScoreAnchors)
• Fix bug in FindClusters() when the last node has no edges
• Default to weighted = TRUE when constructing igraph objects in RunLeiden. Remove corresponding weights parameter from FindClusters().
• Fix handling of keys in FeatureScatter()
• Change CellSelector to use Shiny gadgets instead of SDMTools
• Mark PointLocator as defunct
• Remove SDMTools
• Fixed data slot return in AverageExpression when subsetting features and returning a Seurat object

Additions

• Added ability to create a Seurat object from an existing Assay object, or any
  object inheriting from the Assay class
• Added ability to cluster idents and group features in DotPlot
• Added ability to use RColorBrewer plaettes for split DotPlots
• Added visualization and analysis functionality for spatially resolved datasets (Visium, Slide-seq).

Version 3.1.5

Changes

• Replace wilcox.test with limma implementation for a faster FindMarkers default method
• Better point separation for VlnPlots when using the split.by option
• Efficiency improvements for anchor pairing
• Deprecate redundant sort.cell parameter in FeaturePlot
• Fixes to ensure correct class of Matrix passed to c++ functions
• Fixes for underscores in ident labels for DotPlot
• Ensure preservation of matrix dimnames in SampleUMI
• Fix non-standard evaluation problems in subset and WhichCells
• Default split violin option is now a multi group option
• Preserve alpha in FeaturePlot when using blend
• Update assay.used slot for DimReducs when Assay is renamed

Additions:

• New scale parameter in DotPlot
• New keep.sparse parameter in CreateGeneActivityMatrix for a more memory efficient option
• Added ability to store model learned by UMAP and project new data
• New stip.suffix option in Read10X
• Added group.by parameter to FeatureScatter

Version 3.1.4

Changes:

• Fixes to DoHeatmap to remain compatible with ggplot2 v3.3
• Adoption of patchwork framework to replace CombinePlots

Version 3.1.3

Changes:

• Export CellsByIdentites and RowMergeSparseMatrices
• nCount and nFeature metadata variables retained after subset and updated properly with UpdateSeuratObject
• Fix uwot support for running directly on feature matrices
• Fixes for keys with underscores
• Fix issue with leiden option for FindClusters
• Fix for data transfer when using sctransform
• SDMTools moved to Suggests as package is orphaned

Additions:

• New system-agnostic executable locator to fix FIt-SNE problem on Windows

Version 3.1.2

Changes:

• Only run CalcN (generates nFeatures and nCounts) when counts changes
• Fix issue regarding colons in feature names
• Change object class testing to use inherits or is.* for R 4.0 compatability

Additions:

• New RegroupIdents function to reassign idents based on metadata column majority
• UpdateSymbolList function to pull new gene names from HGNC
• Added support for H5AD layers as additional assays in a Seurat object