NEWS.md
Load10X_Spatial, Read10X_Image,GetTissueCoordinates.VisiumV2
SpatialPlot, SingleSpatialPlot, SpatialDimPlot, SpatialFeaturePlot
Read10X_Segmentations, Read10X_HD_GeoJson, Format10X_GeoJson_CellID
InteractiveSpatialPlot to allow users to interactively lasso-select cells from a spatial Seurat object (Visium, SlideSeq, or Vizgen 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).FetchData as previously; added warning to alert users when column names of metadata and dimensionality reduction embeddings conflictLabelClusters for consistent cluster label coloring (#10198)cluster_leiden from igraph when running Leiden clustering (#9931)umap2 from uwot when running UMAP (#9918)approx_pow parameter from uwot when running UMAP (#9449)LoadXenium to add support for Xenium protein data (#10024)FeaturePlot (#10053)label.size.cutoff parameter to DimPlot to allow users to label only clusters above a certain size (#10092)GetAssayData and PackageCheck (#9924), (#10102)RunAzimuth relating to FindTransferAnchors (#9924)LeverageScore relating to handling of (variable) features (#9924)PseudobulkExpression to acccount for the case that a category passed to group.by has only one value (#10092)VlnPlot to use assay passed to the function if specified (#10092)FeatureScatter to allow gene names with parentheses to be plotted (#10092)SingleRasterMap to store object metadata correctly (#10092)FindClusters to order cluster factor levels correctly when assigning a custom cluster name (#10092)FindConservedMarkers to remove NA values (#9917)guides, aes_string, and facet_grid deprecation warnings (#9409, #10116)DimPlot bug where metadata columns named ‘PC_1’, ‘UMAP_1’ etc override reduction embeddings (#10062)PseudobulkExpression to forward relevant arguments to NormalizeData (#9840)FindSpatiallyVariableFeatures; deprecated the slot parameter in favor of layer (#9836)FindTransferAnchors’s reference argument to accept SCT inputs containing more than one SCT model; in this case, the reference model that was fit against the largest number of cells is used (#9833)FindTransferAnchors’s query argument to accept multi-layer inputs; updated MappingScore to support multi-layer query inputs (#9832)LeverageScore.default to convert BPCells::IterableMatrix inputs with less than 7500 cells into a sparse matrix before performing the calculation (#9831)VariableFeatures setter from SketchData (#9830)Cells.SCTAssay’s layer argument accept slot names: "counts", "data", "scale.data"; enabled compatibility with SketchData/LeverageScore(#9830)SCTransform.StdAssay to simplify and speed up the method (#9828)AddModuleScore to support multi-layer inputs (#9826)PseudobulkExpression to work with Seurat inputs containing more than one assay (9824)RunICA.StdAssay (#9825)HarmonyIntegration to call harmony::RunHarmony in favor of the deprecated harmony::HarmonyMatrix (#9789)raster.dpi parameter to VlnPlot (#9665)SpatialDimPlot(..., interactive = TRUE) to support SlideSeq and STARmap input types; added ScaleFactors.SlideSeq & ScaleFactors.STARmap generics (#9691)PercentageFeatureSet so that the assay parameter is always respected; fixed PercentageFeatureSet to raise a warning if any features are absent in the specified assay instead of throwing an error (#9686)GroupCorrelation and GroupCorrelationPlot to be compatible with SeuratObject >= 5.0.0 (#9625)test_find_clusters.R to accommodate variability in label assignments given by FindClusters across different systems (#9641)group.by parameter to FindAllMarkers, allowing users to regroup their data using a non-default identity class prior to performing differential expression (#9550)image.type parameter to Read10X_Image enabling VisiumV1 instances to be populated instead of instances of the default VisiumV2 class (#9556)IntegrateLayers to respect the dims.to.integrate parameterstroke.size parameter to DimPlot (#8180)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)RunPCA to use the BPCells-provided SVD solver on BPCells matrices; updated JackStraw to support BPCells matrices (#8271)RunPCA to avoid converting BPCells matrices into dense matrices - significantly reduces the function’s memory usage when running on BPCells matrices (#8966)RunSLSI to support BPCells matricesDietSeurat so that the layers parameter is respected (#8197)RunUMAP to support umap-learn version >= 0.5.0 (#9559)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)LoadXenium to accommodate datasets without “Blank Codeword” or “Unassigned Codeword” matrices(#9135)ReadXenium to properly parse multiple molecular outputs at once (#8265)features parameter to LeverageScore and SketchData
SketchData’s ncells parameter to accept integer vectorSpatialDimPlots to display spatial coordinatesBuildClusterTree to PseudobulkExpression(..., method = "aggregate") instead of AverageExpression
SpatialPlot to properly handle images with shared cellscluster.name parameter to BuildNicheAssay
VisiumV2 class, inherits SeuratObject::FOV, returned by Load10X_Spatial
Load10X_Spatial to support loading Visium HD datasets - added bin.size parameterRead10X_Coordinates to handle new tissue_coordinates.parquet filesshape parameter to SpatialPlot and wrappers: SpatialFeaturePlot and SpatialDimPlot
image.scale parameter to SpatialPlot and related functions: SpatialFeaturePlot/ISpatialFeaturePlot and SpatialDimPlot/ISpatialDimPlot
image.name parameter to Read10X_Image
scale parameter to Radius.VisiumV1
spot.radius attribute for VisiumV1 instance returned by Read10X_Image — replace scale.factors$fiducial with scale.factors$spot
Read10X_Coordinates and Read10X_ScaleFactors
SpatialPlot to properly handle mutli-assay Seurat instancesPercentAbove to discount null values (#8412)log parameter to FeatureScatter
clip.range for SCTransform when ncells is less than the size of the passed datasetSCTransform.StdAssay to pass extra arguments to sctransform::vst(). Fixes #875
PseudobulkExpression by adding ‘g’ to cell names that started with numeric valuesPseudobulkExpression by adding each variable specified in group.by as columns in the object metadata when return.seurat=TRUE
DimPlot and FeatureScatter which were breaking when using the split.by argument with a variable that contained NAsBridgeCellsRepresentation to construct a dictionary representation for each unimodal dataset.BuildNicheAssay to construct a new assay where each feature is a cell label. The values represent the sum of a particular cell label neighboring a given cell.CalcDispersion to calculate the dispersion of features.CCAIntegration to perform Seurat-CCA Integration.CountSketch to generate a CountSketch random matrix.CreateCategoryMatrix to create a one-hot matrix for a given label.DISP to find variable features based on dispersion.FastRPCAIntegration as a convenience wrapper function around the following three functions that are often run together when performing integration.FetchResiduals_reference as a temporary function to get residuals from the reference.FetchResiduals to call sctransform::get_residuals.FetchResidualSCTModel to calculate Pearson residuals of features not in the scale.data.FindBridgeAnchor to find bridge anchors between two unimodal datasets.FindBridgeIntegrationAnchors to find a set of anchors for integration between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.FindBridgeTransferAnchors to find a set of anchors for label transfer between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.GaussianSketch to perform Gaussian sketching.HarmonyIntegration to perform Harmony integration.IntegrateLayers to integrate layers in an assay object.JointPCAIntegration to perform Seurat-Joint PCA Integration.LeverageScore to compute the leverage scores for a given object.LoadCurioSeeker to load Curio Seeker data.MVP to find variable features based on mean.var.plot.NNtoGraph to convert the Neighbor class to an asymmetrical Graph class.PrepareBridgeReference to preprocess the multi-omic bridge and unimodal reference datasets into an extended reference.ProjectCellEmbeddings to project query data onto the reference dimensional reduction.ProjectData to project high-dimensional single-cell RNA expression data from a full dataset onto the lower-dimensional embedding of the sketch of the dataset.ProjectDimReduc to project query data to reference dimensional reduction.ProjectIntegration to integrate embeddings from the integrated sketched.assay.PseudobulkExpression to normalize the count data present in a given assay.Read10X_probe_metadata to read the probe metadata from a 10x Genomics probe barcode matrix file in HDF5 format.RPCAIntegration to perform Seurat-RPCA Integration.RunGraphLaplacian to run a graph Laplacian dimensionality reduction.SelectIntegrationFeatures5 to select integration features for v5 assays.SelectSCTIntegrationFeatures to select SCT integration features.SketchData to use sketching methods to downsample high-dimensional single-cell RNA expression data for help with scalability for large datasets.TransferSketchLabels to transfer cell type labels from a sketched dataset to a full dataset based on the similarities in the lower-dimensional space.UnSketchEmbeddings to transfer embeddings from sketched cells to the full data.VST to apply a variance stabilizing transformation for selection of variable features.PrepSCTFindMarkers
LoadNanostring(#7566)as.Seurat.SingleCellExperiment() (#6692)LoadCurioSeeker to load sequencing-based spatial datasets generated using the Curio Seekerpt.size bug when rasterization is set to true (#7379)FoldChange and FindMarkers to support all normalization approaches (#7115,#7110,#7095,#6976,#6654,#6701,#6773, #7107)ReadParseBio (#7565)ReadMtx() to add back missing parametersSCTransform() for V5 assays to retain gene attributes (#7557)LeverageScore() for objects with few features (#7650
FindMarkers() when run post Integration/Transfer (#6856)spatstat.core with spatstat.explore
FindMarkers() when using SCT assay (#6856)DoHeatmap() (#5783)ScaleData() when regressing out one gene (#5970)PlotPerturbScore() (#6081)SpatialDimPlot() when using group.by (#6179)add.noise parameter in VlnPlot() (#5756)pseudocount.use in differential expression functions to be set at the Assay levelgiveCsparse related warnings in Read10X_h5
SpatialPlot (#5774)ReadMtx on Windows (#5687)VlnPlot to switch on rasterization only when required (#5846)ncol behavior in SpatialPlot (#5774)jitter to FALSE in FeatureScatter (#5876)Cells methods to new signature (x, ...)default.stringsAsFactors() with getOption("stringsAsFactors")
raster.dpi parameter to DimPlot/FeaturePlot to optionally rasterize individual points (#5392)ReadParseBio to support split-pipe 0.9.6p (#5446)split.by in FeaturePlot() (#5243)raster parameter to VlnPlot to optionally rasterize individual points (#5076)min.cells.group parameter to FindConservedMarkers (#5079)do.center to FALSE for lsiproject in FindTransferAnchors
ReadMtx() (#5158)label.color parameter to FeaturePlot (#5314)ProjectUMAP (#5257, #5104, #5373)reduction parameter to BuildClusterTree() (#4598)RunUMAP() (#4630)image parameter to Load10X_Spatial() and image.name parameter to Read10X_Image() (#4641)ReadSTARsolo() function to read output from STARsolodensify parameter to FindMarkers()
ReadParsebio() function to read output from Parse Biosciencesimage.alpha parameter to SpatialDimPlot() and SpatialFeaturePlot()
RunUMAP (#4972)FindSpatiallyVariableFeatures() (#4611)FindVariableFeatures() when using selection.method = "mvp" and binning.method = "equal_frequency" (#4712)DoHeatmap() to remove random characters from plot legend(#4660)RunCCA()
VariableFeaturePlot()
jitter parameter to FeatureScatter()
as.SingleCellExperiment.Seurat() for the latest verion of SingleCellExperiment (#4532)MapQuery()
UpdateSymbolList(), no longer searches aliases and exposes the search.types parameter in GeneSymbolThesarus() (#4545)scale.data slot as well when converting with as.SingleCellExperiment.Seurat()
alpha parameter for SpatialDimPlot()
as.SingleCellExperiment.Seurat() conversion for atypical reducedDim componentsAddAzimuthScores() and AddAzimuthResults() functionsshuffle parameter to FeatureScatter() (#4280)lsiproject and rpca options for FindTransferAnchors()
rlsi option for FindIntegrationAnchors()
SingleCellExperiment to SeuratObject class (#4205)SingleCellExperiment to SeuratObject class (#3764)score.thresh parameter in ScoreJackStraw() (#4268)FindMarkers() non-log transformed data.RunUMAP()
DotPlot to use log1p when scale=False (#4298)DimPlot
ident.1 in FindMarkers()
FindIntegrationAnchors()
fc.name parameter in FindMarkers() (#4474)group.by parameter in PlotPerturbScore() in favor of mixscape.class.PlotClusterTree()
cols parameter to JackStrawPlot()
ReadMtx() to read local and remote mtx files with associated cell and feature name filesFindMarkers (e.g, >= logfc.threshold rather than >)Read10X() now prepends dataset number for first dataset when reading multiple datasetssubset.AnchorSet()
FindMarkers() when setting a different pseudocount (#4111)RunLDA() related to proper passing of assay parameter.order=TRUE in SingleDimPlot(), print NA points under all others.data.dir in Read10X()
RunUMAP now checks for graph/neighbor consistencyFoldChange() component in FindMarkers().merge.DimReduc methodIntegrateEmbeddings() to correct embeddings of DimReducsProjectUMAP() to project query cells into a reference UMAP spaceMapQuery() as a wrapper around IntegrateData(), IntegrateEmbeddings(), and ProjectUMAP()
MappingScore to compute a per-cell mapping score used in AzimuthAggregateExpression() for summation based pseudobulk calculationsCalcPerturbSig(), PrepLDA(), RunLDA(), DEenrichRPlot(), MixscapeHeatmap(), MixscapeLDA(), PlotPerturbScore(), RunMixscape()
FindSubCluster() to further cluster existing clustersRunSPCA()
FindMultiModalNeighbors()
NNPlot().PredictAssay() to impute expression or embeddings from nearest neighborsGraphs() function to access the names of the stored Graph objects or pull a specific oneAnnotateAnchors() to aid in AnchorSet interpretation as well as subset.AnchorSet()
Read10X()
FeatureScatter() and VariableFeaturePlot()
PrepVSTResults()
ncells parameter in SCTransform() changed to 5000FindMarkers() changed from ln to log2AverageExpression()
AnchorSet class re-implemented as a virtual class from which IntegrationAnchorSet and TransferAnchorSet now inherit.VlnPlot() now set automatically if not specifiedas.character.quosure usage with as_label due to deprecationDimPlot() and FeaturePlot() changed from 50,000 to 100,000SCTransform() now returns a formalized Assay subclass SCTAssay()
normalization.method='SCT' in FindTransferAnchors(), normalize query using reference SCT model when possible.FindNeighbors to Assay.nn
CreateGeneActivityMatrix replaced by Signac::GeneActivity()
RunLSI replaced by by Signac::RunTFIDF() and Signac::RunSVD()
ReadAlevin and ReadAlevinCsv moved to SeuratWrappersExportToCellbrowser and StopCellbrowser moved to SeuratWrappersDimPlot when specifying group.by parameterkeep.scale parameter added to FeaturePlot to control scaling across multiple features and/or splits.Same deprecated in favor of base::identity
DietSeurat to work with specialized Assay objectsape implementation of Moran’s IKey<-.DimReduc that allow handling of empty reduction column namesctrl in CellCycleScoring
export(rng=FALSE) to avoid potential future warningsSetHighlight in plotsdo.cpp deprecated and will default to trueWhichCells regardless of whether or not idents is passedCreateAssayObject() when data.frame has no rownames.return.model parameter in RunUMAP()
DoHeatmap()
label.color and label.box parameters to DimPlot
shuffle and seed parameters to DimPlot() to help with overplottingslot parameter in RunUMAP
Spatial*Plot when running with interactive=TRUETop and remove duplicate items when balanced=TRUEdo.call()
RunPCA()
CellSelector
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 SeuratDiskas.loom and as.Seurat.loom deprecated in favor of functionality found in SeuratDiskDotPlot
DotPlots
add.iter parameter from RunTSNE functionDoHeatmap group bar + labelsScoreAnchors)FindClusters() when the last node has no edgesRunLeiden. Remove corresponding weights parameter from FindClusters().FeatureScatter()
CellSelector to use Shiny gadgets instead of SDMToolsPointLocator as defunctSDMTools
AverageExpression when subsetting features and returning a Seurat objectscale parameter in DotPlot
keep.sparse parameter inCreateGeneActivityMatrix` for a more memory efficient optionstrip.suffix option in Read10X. This changes the default behavior of Read10X. A trailing -1 present in all cell names will not be removed by default.group.by parameter to FeatureScatter
VlnPlots when using the split.by optionsort.cell parameter in FeaturePlot
DotPlot
SampleUMI
subset and WhichCells
FeaturePlot when using blend
assay.used slot for DimReducs when Assay is renamedCellsByIdentities and RowMergeSparseMatrices functionsUpdateSeuratObject
FindClusters
RegroupIdents function to reassign idents based on metadata column majorityUpdateSymbolList function to pull new gene names from HGNCSeurat objectobsm and varm stuctureAddModuleScore
MapQuery)PrepSCTIntegration function to facilitate integration after SCTransform
reference parameter in FindIntegrationAnchors
reduction option in FindIntegrationAnchors
CollapseEmbeddingOutliers functionFindTransferAnchors after SCTransform
ColorDimSplit functionalityCheckDots to catch unused parameters and suggest updated namesReductions and Assays assays functions to list stored DimReducs and AssaysLogSeuratCommand
Read10X
ReadH5AD to distinguish FVF methodsAssay specification in BuildClusterTree
FeaturePlot when using both blend and split.by
WhichCells when passing cells and invert
HoverLocator labels and title|)RunLSI and RunALRA
ExIPlot
FindClusters
FeaturePlotsGetResidual functionSeurat objectDimReduc object column namesDoHeatmap
FeaturePlot
SingleDimPlot
FindClusters
DimPlot
levels<-.Seurat
BuildClusterTree
ScaleData