|
a |
|
b/man/getClusters.Rd |
|
|
1 |
% Generated by roxygen2: do not edit by hand |
|
|
2 |
% Please edit documentation in R/clustering.R |
|
|
3 |
\name{getClusters} |
|
|
4 |
\alias{getClusters} |
|
|
5 |
\title{getClusters} |
|
|
6 |
\usage{ |
|
|
7 |
getClusters( |
|
|
8 |
object, |
|
|
9 |
resolution = 1, |
|
|
10 |
nclus = integer(0), |
|
|
11 |
assay = NULL, |
|
|
12 |
method = "leiden", |
|
|
13 |
label = "clusters", |
|
|
14 |
graph = "kNN", |
|
|
15 |
seed = 1, |
|
|
16 |
abundance_limit = 2 |
|
|
17 |
) |
|
|
18 |
} |
|
|
19 |
\arguments{ |
|
|
20 |
\item{object}{a VoltRon object} |
|
|
21 |
|
|
|
22 |
\item{resolution}{the resolution parameter for leiden clustering.} |
|
|
23 |
|
|
|
24 |
\item{nclus}{The number of cluster centers for K-means clustering.} |
|
|
25 |
|
|
|
26 |
\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. |
|
|
27 |
if NULL, the default assay will be used, see \link{vrMainAssay}.} |
|
|
28 |
|
|
|
29 |
\item{method}{The method of clustering. Use 'leiden' to perform graph clustering and 'kmeans' for K-means based clustering} |
|
|
30 |
|
|
|
31 |
\item{label}{the name for the newly created clustering column in the metadata} |
|
|
32 |
|
|
|
33 |
\item{graph}{the graph type to be used} |
|
|
34 |
|
|
|
35 |
\item{seed}{seed} |
|
|
36 |
|
|
|
37 |
\item{abundance_limit}{the minimum number of points for a cluster, hence clusters with abundance lower than this limit will be appointed to other nearby clusters} |
|
|
38 |
} |
|
|
39 |
\description{ |
|
|
40 |
Get clustering of the VoltRon object |
|
|
41 |
} |