Version 4.0.5

Changes

• Update documentation for to.upper parameter in Load10X_Spatial() (#4576)
• Update concept tags for RunSPCA() (#4978)
• Conditionally run tests/packages that use suggested packages (#5160)

Version 4.0.4

Changes

• Warn and continue rather than erroring if not all features are available in FindSpatiallyVariableFeatures() (#4611)
• Bug fix for SCT-based integration in selecting proper reference model (#4355)
• Bug fix for reading from absolute paths in ReadMtx (#4723)
• Bug fix in SingleCellExperiment conversion (#4633)
• Bug fix in FindVariableFeatures() when using selection.method = "mvp" and binning.method = "equal_frequency" (#4712)
• Bug fix in DoHeatmap() to remove random characters from plot legend(#4660)
• Fix cell renaming in RunCCA()
• Fix issue in SingleCellExperiment conversion where the mainExp would not be set properly
• Fix for default dispersion info displayed in VariableFeaturePlot()

Additions

• Add reduction parameter to BuildClusterTree() (#4598)
• Add DensMAP option to RunUMAP() (#4630)
• Add image parameter to Load10X_Spatial() and image.name parameter to Read10X_Image() (#4641)
• Add ReadSTARsolo() function to read output from STARsolo
• Add densify parameter to FindMarkers()
• Add ReadParsebio() function to read output from Parse Biosciences
• Add the image.alpha parameter to SpatialDimPlot() and SpatialFeaturePlot()

Version 4.0.3

Changes

• Fix issues with as.SingleCellExperiment.Seurat() for the latest verion of SingleCellExperiment (#4532)
• Ensure proper reference.reduction is used in MapQuery()
• Fix to UpdateSymbolList(), no longer searches aliases and exposes the search.types parameter in GeneSymbolThesarus() (#4545)
• Transfer scale.data slot as well when converting with as.SingleCellExperiment.Seurat()
• Enable alpha parameter for SpatialDimPlot()
• Fix as.SingleCellExperiment.Seurat() conversion for atypical reducedDim components

Additions

• Add jitter parameter to FeatureScatter()

Version 4.0.2

Changes

• Preserve feature metadata when converting from SingleCellExperiment to SeuratObject class
  (#4205)
• Preserve multiple assays when converting from SingleCellExperiment to SeuratObject class
  (#3764)
• Fix passing of score.thresh parameter in ScoreJackStraw() (#4268)
• Fix FC calculation in FindMarkers() non-log transformed data.
• Add umap-learn version >= 0.5.0 compatibility for RunUMAP()
• Fix DotPlot to use log1p when scale=False
  (#4298)
• Fix split and shuffled DimPlot
• Disallow NULL or another length 0 vector for ident.1 in FindMarkers()
• Fix range shift when labeling clusters on a GeomSpatial plot
• Fix SpatialPlot distortion for non-square images.
• Fix future-related warnings in FindIntegrationAnchors()
• Fix fc.name parameter in FindMarkers() (#4474)
• Deprecate group.by parameter in PlotPerturbScore() in favor of mixscape.class.

Additions

• New AddAzimuthScores() and AddAzimuthResults() functions
• Add shuffle parameter to FeatureScatter() (#4280)
• Add lsiproject and rpca options for FindTransferAnchors()
• Add rlsi option for FindIntegrationAnchors()

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).