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`
`pca`	now a synonym for `RunPCA`
`PCA`	now a synonym for `PCA`
`project.pca`	now a synonym for `ProjectPCA`
`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`
`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`
`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`
`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`
`VizClassification`	has been removed without replacement