create_umap: Create a UMAP data.frame from a result object

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

Create a UMAP data.frame from a result object

Usage

create_umap(
  result,
  annotation,
  n_neighbors = 30,
  min_dist = 0.75,
  spread = 1,
  proportional = TRUE,
  seed = FALSE
)

Arguments

result	S4 Result Object
annotation	Annotation to use for umap coloring
n_neighbors	The size of local neighborhood used for views of manifold approximation. Larger values result in more global the manifold, while smaller values result in more local data being preserved. Default 30. See '?uwot::umap' for more information.
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. Default 0.2. See '?uwot::umap' for more information.
spread	The effective scale of embedded points. In combination with ‘min_dist’, this determines how clustered/clumped the embedded points are. Default 1. See '?uwot::umap' for more information.
proportional	Whether weights are normalized to sum to 1 or not
seed	Use a seed for reproducible results

Value

UMAP data.frame

Examples

result <- readRDS(system.file("testdata", "res_annot.rds",
package = "BAGEL"))
BAGEL::create_umap(result = result, annotation = "Tumor_Subtypes",
n_neighbors = 5)

campbio/BAGEL documentation built on Oct. 6, 2020, 3:59 a.m.