compumap: 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
)

Value

SCseq object with umap coordinates stored in slot umap.

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.

Examples

Run this code

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

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