compumap: Computation of a two dimensional umap representation

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Computation of a two dimensional umap representation

Description

This functions performs the computation of a two-dimensional umap representation based on the distance matrix in slot distances using the umap package.

Usage

compumap(
  object,
  dimRed = FALSE,
  n_neighbors = 15,
  metric = "euclidean",
  n_epochs = 200,
  min_dist = 0.1,
  local_connectivity = 1,
  spread = 1
)

Arguments

object	SCseq class object.
dimRed	logical. If TRUE then the umap is computed from the feature matrix in slot dimRed$x (if not equal to NULL). Default is FALSE and the umap is computed from the distance matrix stored in slot distances. If slot distances equals NULL dimRed is automatially set to TRUE.
n_neighbors	Umap parameter. See help(umap.defaults) after loading package umap. Default is 15.
metric	Umap parameter. See help(umap.defaults) after loading package umap. Default is "euclidean".
n_epochs	Umap parameter. See help(umap.defaults) after loading package umap. Default is 200.
min_dist	Umap parameter. See help(umap.defaults) after loading package umap. Default is 0.1.
local_connectivity	Umap parameter. See help(umap.defaults) after loading package umap. Default is 1.
spread	Umap parameter. See help(umap.defaults) after loading package umap. Default is 1.

Value

SCseq object with umap coordinates stored in slot umap.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
sc <- compumap(sc)

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.