Perform community clustering using Phenograph
DoPhenoGraph(object, ...)
# S3 method for Seurat
DoPhenoGraph(object, reduction_use = "pca", k = 30, prefix = "community", ...)
# S3 method for SingleCellExperiment
DoPhenoGraph(object, reduction_use = "pca", k = 30, prefix = "community", ...)A Seurat or SingleCellExperiment object with data to be clustered.
Extra parameters to pass to the phenograph function.
Dimensional reduction to use for clustering calculations (i.e. pca, ica, cca, etc...)
Number of nearest neighbors to use in first step of graph construction. If a list of integers is passed, Phenograph will be Do with each value and the last will be used to set object@ident. Default = 30
String prefix to used as in the column name entered in the meta.data slot
Seurat object
SingleCellExperiment object