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Seurat (version 2.0.0)

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