runLeiden: Run Leiden Algorithm.

In beyondpie/pureRUtils: Commonly used R functions with pure R codes

Run Leiden Algorithm.

Description

Run Leiden Algorithm.

Usage

runLeiden(
  snap = NULL,
  snapFile = NULL,
  r = 0.5,
  pt = "RB",
  seed = 10,
  pathToPython = NULL,
  outLeidenFile = NULL,
  outClusterMetaCSV = NULL,
  outClusterPDF = NULL,
  pdfn = NULL,
  colName = "cluster",
  dims = 1:30,
  umapNcores = 1,
  ...
)

Arguments

snap	SnapObject default NULL
snapFile	characters default NULL
r	numeric resolution paramter for leiden, default 0.5
pt	characters partition type for leiden, default "RB"
seed	integer default NULL
pathToPython	characters where the python is, default NULL
outLeidenFile	characters default NULL
outClusterMetaCSV	characters default NULL
outClusterPDF	characters default NULL
pdfn	function used to draw figures for outClusterPDF the inputs are snap object and others default NULL.
colName	characters used for record cluster namae in snap meta, default is "cluster". if snap@metaData has this column, will use colName.1 instead
dims	integer or vector for UMAP default is 1:30
umapNcores	integer default 1
...	use for pdfn function

Value

SnapObject, slot "cluster" is the result

beyondpie/pureRUtils documentation built on Jan. 10, 2023, 3:22 a.m.