runUMAP: Umap based on ArchR and Seuratdefault parameters
In beyondpie/smmtools: Single-cell multi-omics sequenceing data tools

runUMAP

R Documentation

Umap based on ArchR and Seuratdefault parameters

Description

Use uwot pacakge since it's more stable in R. Uwot::umap default parameters are from ArchR.

Usage

runUMAP(
  dmat,
  sdev = NULL,
  nPC = 30,
  outpdf = NULL,
  width = 7,
  height = 7,
  xlab = "UMAP-1",
  ylab = "UMAP-1",
  title = NULL,
  color = NULL,
  ncomp = 2,
  seed = 10,
  weightDimReduct = FALSE,
  umapNeighbors = 30,
  umapMindist = 0.3,
  umapMetric = "cosine",
  umapVerbose = FALSE,
  umapFastSGD = TRUE,
  umapNthread = 1,
  a = NULL,
  b = NULL,
  init = "spectral",
  retnn = FALSE,
  retmodel = FALSE
)

Arguments

`dmat`	matrix, cell by feature
`sdev`	vector, scaling factors for dims, default is NULL
`nPC`	integer, dims till the nPC-th dim will be used for UMAP, default is 30. When nfeature in mat is less than nPC, nfeature will be used.
`outpdf`	string, default is NULL
`width`	double, for outpdf, default is 7
`height`	double, for outpdf, default is 7
`xlab`	string, default is "UMAP-1"
`ylab`	string, default is "UMAP-2"
`title`	string, default is NULL
`color`	vector of string or factor, default is NULL
`ncomp`	integer, defaul is 2
`seed`	integer, default is 10
`weightDimReduct`	bool, default is FALSE, together used with sdev.
`umapNeighbors`	integer, default is 30 In umot::umap, default is 15.
`umapMindist`	double, default is 0.3 In umot::umap, default is 0.01
`umapMetric`	string, default is "cosine" NOTE: "euclidean" is the default in uwot::umap
`umapVerbose`	bool, default is FALSE
`umapFastSGD`	bool, default is TRUE
`umapNthread`	integer, default is 1
`a`	double, default is NULL
`b`	double, default is NULL NOTE: a = 1.8956, b = 0.8006 is the default UMAP
`init`	string, default is "special" NOTE: Use init = "spca" rather than init = "spectral" for better reproducibility (although the latter is the default and preferred method for UMAP initialization).
`retnn`	bool, default is FALSE
`retmodel`	bool, default is FALSE Set both retnn and retmodel as TRUE to save model