DoPhenoGraph: DoPhenoGraph

In milescsmith/ReductionWrappers: Wrapper exposing several Python dimensional reduction tools

DoPhenoGraph

Description

Perform community clustering using Phenograph

Usage

DoPhenoGraph(object, ...)

## S3 method for class 'Seurat'
DoPhenoGraph(object, reduction_use = "pca", k = 30, prefix = "community", ...)

## S3 method for class 'SingleCellExperiment'
DoPhenoGraph(object, reduction_use = "pca", k = 30, prefix = "community", ...)

Arguments

object	A Seurat or SingleCellExperiment object with data to be clustered.
...	Extra parameters to pass to the phenograph function.
reduction_use	Dimensional reduction to use for clustering calculations (i.e. pca, ica, cca, etc...)
k	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
prefix	String prefix to used as in the column name entered in the meta.data slot

Value

Seurat object

SingleCellExperiment object

milescsmith/ReductionWrappers documentation built on March 25, 2023, 11:58 a.m.