runPhenograph: RphenoGraph clustering

Description Usage Arguments Value Examples

View source: R/cluster.R

Description

A simple R implementation of the phenograph [PhenoGraph](http://www.cell.com/cell/abstract/S0092-8674(15)00637-6) algorithm, which is a clustering method designed for high-dimensional single-cell data analysis. It works by creating a graph ("network") representing phenotypic similarities between cells by calculating the Jaccard coefficient between nearest-neighbor sets, and then identifying communities using the well known [Louvain method](https://sites.google.com/site/findcommunities/) in this graph.

Usage

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runPhenograph(object, knn = 30, scale = FALSE, verbose = FALSE, ...)

Arguments

object

a CYT object.

knn

numeric. Number of nearest neighbours, default is 30.

scale

logical. Whether to scale the expression matrix

verbose

logical. Whether to print calculation progress.

...

Parameters passing to igraph function

Value

A CYT object with cluster

Examples

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cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

cyt <- runPhenograph(cyt, knn = 30, verbose = TRUE)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.