Clustering with Seurat — runSeuratClustering • SPATA2

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

runSeuratClustering(
  object,
  name = "seurat_clusters",
  mtr_name = getActiveMatrixName(object),
  FindVariableFeatures = list(selection.method = "vst", nfeatures = 2000),
  RunPCA = list(npcs = 60),
  FindNeighbors = list(dims = 1:30),
  FindClusters = list(resolution = 0.8)
)

Arguments

FindVariableFeatures, RunPCA, FindNeighbors, FindClusters: Each argument takes a list of arguments that is given to the equivalent function.

Value

The input spata2 object containing the added or computed results.

Examples


 object <- SPATAData::downloadSpataObject("275_T")

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

 plotSurface(object, color_by = "seurat_clusters")