getUMAP: getUMAP

In genesofeve/ProjectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

getUMAP

Description

Function to provide umap of projection

Usage

getUMAP(projection, axis = 2, umapMethod = "naive", umapConfig = umap.defaults)

Arguments

projection	martrix, a projection generated from projectR
axis	integer, either 1 umap of projection or 2 for umap of transpose of projection
umapMethod	character, implementation. Available methods are 'naive' (an implementation written in pure R) and 'umap-learn' (requires python package 'umap-learn')
umapConfig	umap.config, a list of parameters to customize umap embedding

Value

A umap of projection

Examples

library(umap)
projection <- projectR(data=p.ESepiGen4c1l$mRNA.Seq,loadings=AP.RNAseq6l3c3t$Amean,
dataNames = map.ESepiGen4c1l[["GeneSymbols"]], full = TRUE)
umapConfig = umap.defaults
umapConfig$n_neighbors = 3
projectionUMAP <- getUMAP(projection,umapConfig = umapConfig)

genesofeve/ProjectR documentation built on Nov. 16, 2024, 8:20 p.m.