runPhenograph {CytoTree} | R Documentation |
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.
runPhenograph(object, knn = 30, scale = FALSE, verbose = FALSE, ...)
object |
an 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 |
An CYT object with cluster
cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree") cyt <- readRDS(file = cyt.file) cyt <- runPhenograph(cyt, knn = 30, verbose = TRUE)