AutoNumber.by.PrinCurve: AutoNumber.by.PrinCurve

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

AutoNumber.by.PrinCurve

Description

Relabel cluster numbers along the principal curve of 2 UMAP (or tSNE) dimensions. #

Usage

AutoNumber.by.PrinCurve(
  obj = combined.obj,
  dim = 1:2,
  plotit = TRUE,
  swap = -1,
  reduction = "umap",
  res = "integrated_snn_res.0.5"
)

Arguments

obj	Seurat object, Default: combined.obj
dim	Dimensions to use, Default: 1:2
plotit	Plot results (& show it), Default: TRUE.
swap	Swap Lambda paramter (multiplied with this) , Default: -1
reduction	UMAP, tSNE, or PCA (Dim. reduction to use), Default: 'umap'
res	Clustering resoluton to use, Default: 'integrated_snn_res.0.5'

See Also

principal_curve

Examples

## Not run: 
if (interactive()) {
  DimPlot.ClusterNames(ident = "integrated_snn_res.0.5")
  combined.obj <- AutoNumber.by.PrinCurve(
    obj = combined.obj, dim = 1:2, reduction = "umap", plotit = TRUE,
    swap = -1, res = "integrated_snn_res.0.5"
  )
  DimPlot.ClusterNames(ident = "integrated_snn_res.0.5.prin.curve")
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.