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

setup(...)

Arguments

...

Parameters to be passed to the modern version of the function

Details

`setup`	now a synonym for `Setup`
`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 `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 a synonym for `SubsetCells`
`project.samples`	now a synonym for `ProjectSamples`
`run_diffusion`	now a synonym for `RunDiffusion`
`ica`	now a synonym for `ICA`
`cluster.alpha`	now a synonym for `ClusterAlpha`
`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`
`getWeightMatrix`	now a synonym for `GetWeightMatrix`
`regulatorScore`	now a synonym for `RegulatorScore`
`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 a synonym for `GeneScorePlot`
`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`