NEWS.md
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