Seurat-deprecated: Deprecated function(s) in the Seurat package
In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

Description Usage Arguments Details

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

1	vlnPlot(...)

...

Parameters to be passed to the modern version of the function

`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`	has been removed and may be replaced at a later date
`add_samples`	now a synonym for `AddSamples`
`subsetCells`	now deleted
`project.samples`	has been removed and may be replaced at a later date
`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`	has been removed and may be restored at a later date
`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`	has been deprecated
`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`	has been removed without replacement
`calcNoiseModels`	has been removed and may be replaced at a later date
`feature.plot.keynote`	has been removed without replacement
`feature.heatmap`	now a synonym for `FeatureHeatmap`
`ica.plot`	now a synonym for `ICAPlot`
`dim.plot`	now a synonym for `DimPlot`
`spatial.de`	has been removed and may be replaced at a later date
`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`	has been removed and may be replaced at a later date
`gene.cor.matrix`	has been removed and may be replaced at a later date
`calinskiPlot`	has been removed and may be replaced at a later date
`dot.plot`	now a synonym for `DotPlot`
`addMetaData`	now a synonym for `AddMetaData`
`removePC`	has been removed and may be replaced at a later date
`geneScorePlot`	now deleted
`cellPlot`	now a synonym for `CellPlot`
`jackStraw.permutation.test`	has been deleted
`jackStrawMC`	has been deleted
`jackStrawFull`	has been deleted
`PCAFast`	now a synonym for `PCA`
`writ.table`	has been removed without replacement
`jackRandom`	has been removed without replacement
`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`