Clustering with Seurat

A wrapper around the Seurat clustering pipeline suggested by Hao and Hao et al., 2021.

runSeuratClustering(
  object,
  name = "seurat_clusters",
  mtr_name = activeMatrix(object),
  assay_name = activeAssay(object),
  NormalizeData = list(),
  ScaleData = list(),
  FindVariableFeatures = list(selection.method = "vst", nfeatures = 2000),
  RunPCA = list(npcs = 60),
  FindNeighbors = list(dims = 1:30),
  FindClusters = list(resolution = 0.8),
  prefix = "S",
  overwrite = FALSE
)

Arguments

FindVariableFeatures, RunPCA, FindNeighbors, FindClusters

Each argument takes a list of arguments that is given to the equivalent function.

Value

The updated input object, containing the added, removed or computed results.

Examples

library(SPATA2)

data("example_data")

object <- example_data$object_UKF269T_diet

object <- runSeuratClustering(object, name = "new_seurat_clst")

plotSurface(object, color_by = "new_seurat_clst")