runUmap: Creates UMAP embedding

In navinlabcode/copykit: CopyKit

Creates UMAP embedding

Description

Creates a umap embedding using the package uwot from the segment ratios values

Usage

runUmap(
  scCNA,
  assay = "logr",
  seed = 17,
  min_dist = 0,
  n_neighbors = 50,
  name = "umap",
  ncomponents = 2,
  ...
)

Arguments

scCNA	scCNA object.
assay	String with the name of the assay to pull data from to make the embedding.
seed	Sets a seed for the pseudorandom number generator.
min_dist	The effective minimum distance between embedded points. Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the spread value, which determines the scale at which embedded points will be spread out. See umap.
n_neighbors	The size of local neighborhood (in terms of number of neighboring sample points) used for manifold approximation. Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. See umap.
name	String specifying the name to be used to store the result in the reducedDims of the output.
ncomponents	The dimension of the space to embed into. See umap.
...	Additional parameters passed to umap.

Value

A reduced dimension representation with UMAP in the slot reducedDim from scCNA object. Access reduced dimensions slot with: reducedDim(scCNA, 'umap', withDimnames = FALSE)

Author(s)

Darlan Conterno Minussi

Examples

copykit_obj <- copykit_example_filtered()
copykit_obj <- runUmap(copykit_obj)

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.