Seurat-deprecated: Deprecated function(s) in the Seurat package

Description

These functions are provided for compatibility with older version of the Seurat package. They may eventually be completely removed.

Usage

vlnPlot(...)

Arguments

...

Parameters to be passed to the modern version of the function

Details

`vlnPlot`	now a synonym for `VlnPlot`
`subsetData`	now a synonym for `SubsetData`
`mean.var.plot`	now a synonym for `MeanVarPlot`
`pca`	now a synonym for `RunPCA`
`PCA`	now a synonym for `PCA`
`project.pca`	now a synonym for `ProjectPCA`
`print.pca`	now a synonym for `PrintPCA`
`viz.pca`	now a synonym for `VizPCA`
`set.ident`	now a synonym for `SetIdent`
`pca.plot`	now a synonym for `PCAPlot`
`pcHeatmap`	now a synonym for `PCHeatmap`
`jackStraw`	now a synonym for `JackStraw`
`jackStrawPlot`	now a synonym for `JackStrawPlot`
`run_tsne`	now a synonym for `RunTSNE`
`tsne.plot`	now a synonym for `TSNEPlot`
`find.markers`	now a synonym for `FindMarkers`
`find_all_markers`	now a synonym for `FindAllMarkers`
`genePlot`	now a synonym for `GenePlot`
`feature.plot`	now a synonym for `FeaturePlot`
`buildClusterTree`	now a synonym for `BuildClusterTree`
`plotClusterTree`	now a synonym for `PlotClusterTree`
`plotNoiseModel`	now a synonym for `PlotNoiseModel`
`add_samples`	now a synonym for `AddSamples`
`subsetCells`	now deleted
`project.samples`	now a synonym for `ProjectSamples`
`run_diffusion`	now a synonym for `RunDiffusion`
`ica`	now a synonym for `RunICA`
`ICA`	now a synonym for `RunICA`
`cluster.alpha`	now a synonym for `AverageDetectionRate`
`reorder.ident`	now a synonym for `ReorderIdent`
`average.pca`	now a synonym for `AveragePCA`
`average.expression`	now a synonym for `AverageExpression`
`icTopGenes`	now a synonym for `ICTopGenes`
`pcTopGenes`	now a synonym for `PCTopGenes`
`pcTopCells`	now a synonym for `PCTopCells`
`fetch.data`	now a synonym for `FetchData`
`viz.ica`	now a synonym for `VizIca`
`regulatorScore`	now deleted
`find.markers.node`	now a synonym for `FindMarkersNode`
`diffExp.test`	now a synonym for `DiffExpTest`
`tobit.test`	now a synonym for `TobitTest`
`batch.gene`	now a synonym for `BatchGene`
`marker.test`	now a synonym for `MarkerTest`
`diff.t.test`	now a synonym for `DiffTTest`
`which.cells`	now a synonym for `WhichCells`
`set.all.ident`	now a synonym for `SetAllIdent`
`rename.ident`	now a synonym for `RenameIdent`
`posterior.plot`	now a synonym for `PosteriorPlot`
`map.cell`	now a synonym for `MapCell`
`get.centroids`	now a synonym for `GetCentroids`
`refined.mapping`	now a synonym for `RefinedMapping`
`initial.mapping`	now a synonym for `InitialMapping`
`calc.insitu`	now a synonym for `CalcInsitu`
`fit.gene.k`	now a synonym for `FitGeneK`
`fit.gene.mix`	now a synonym for `FitGeneMix`
`addSmoothedScore`	now a synonym for `AddSmoothedScore`
`addImputedScore`	now a synonym for `AddImputedScore`
`getNewScore`	now a synonym for `GetNewScore`
`calcNoiseModels`	now a synonym for `CalcNoiseModels`
`feature.plot.keynote`	now a synonym for `FeaturePlotKeynote`
`feature.heatmap`	now a synonym for `FeatureHeatmap`
`ica.plot`	now a synonym for `ICAPlot`
`dim.plot`	now a synonym for `DimPlot`
`spatial.de`	now a synonym for `SpatialDe`
`DBclust_dimension`	now a synonym for `DBClustDimension`
`Kclust_dimension`	now a synonym for `KClustDimension`
`pca.sig.genes`	now a synonym for `PCASigGenes`
`doHeatMap`	now a synonym for `DoHeatMap`
`icHeatmap`	now a synonym for `ICHeatmap`
`doKMeans`	now a synonym for `DoKMeans`
`genes.in.cluster`	now a synonym for `GenesInCluster`
`kMeansHeatmap`	now a synonym for `KMeansHeatmap`
`cell.cor.matrix`	now a synonym for `CellCorMatrix`
`gene.cor.matrix`	now a synonym for `GeneCorMatrix`
`calinskiPlot`	now a synonym for `CalinskiPlot`
`dot.plot`	now a synonym for `DotPlot`
`addMetaData`	now a synonym for `AddMetaData`
`removePC`	now a synonym for `RemovePC`
`geneScorePlot`	now deleted
`cellPlot`	now a synonym for `CellPlot`
`jackStraw.permutation.test`	now a synonym for `JackStrawPermutationTest`
`jackStrawMC`	now a synonym for `JackStrawMC`
`jackStrawFull`	now a synonym for `JackStrawFull`
`PCAFast`	now a synonym for `PCA`
`writ.table`	is delteded without replacement
`jackRandom`	now a synonym for `JackRandom`
`MeanVarPlot`	now a synonym for `FindVariableGenes`
`myPalette`	now a synonym for `CustomPalette`
`minusr`	now a synonym for `SubsetRow`
`minusc`	now a synonym for `SubsetColumn`
`RegressOut`	now part of `ScaleData`