These functions are provided for compatibility with older version of the Seurat package. They may eventually be completely removed.
setup(...)
Parameters to be passed to the modern version of the function
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 |