reducedDimSNF: reducedDimSNF

In SydneyBioX/CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

reducedDimSNF

Description

A function to reduce the dimension of the similarity matrix

Usage

reducedDimSNF(sce, metadata = "SNF_W", method = "UMAP", dimNames = NULL, ...)

Arguments

sce	A singlecellexperiment object
metadata	indicates the meta data name of affinity matrix to virsualise
method	the method of visualisation, which can be UMAP, tSNE and diffusion map
dimNames	indicates the name of the reduced dimension results.
...	other parameters for tsne(), umap()

Value

A SingleCellExperiment object

Examples

data(sce_control_subset, package = "CiteFuse")
sce_control_subset <- CiteFuse(sce_control_subset)
sce_control_subset <- reducedDimSNF(sce_control_subset,
method = "tSNE",
dimNames = "tSNE_joint")

SydneyBioX/CiteFuse documentation built on Feb. 13, 2023, 6:04 a.m.