umap {umap}

Computes a manifold approximation and projection

Description

Computes a manifold approximation and projection

Usage

umap(
  d,
  config = umap.defaults,
  method = c("naive", "umap-learn"),
  preserve.seed = TRUE,
  ...
)

Arguments

d

matrix, input data

config

object of class umap.config

method

character, implementation. Available methods are 'naive' (an implementation written in pure R) and 'umap-learn' (requires python package 'umap-learn')

preserve.seed

logical, leave TRUE to insulate external code from randomness within the umap algorithms; set FALSE to allow randomness used in umap algorithms to alter the external random-number generator

...

list of settings; values overwrite defaults from config; see documentation of umap.default for details about available settings

Value

object of class umap, containing at least a component with an embedding and a component with configuration settings

Examples

# embedd iris dataset using default settings
iris.umap = umap(iris[,1:4])

# display object summary
iris.umap

# display embedding coordinates
head(iris.umap$layout)