runUMAP {CytoTree} | R Documentation

## Calculating UMAP

### Description

Calculate Uniform Manifold Approximation and Projection in CYT

### Usage

    runUMAP(
      object,
      umap.config = umap.defaults,
      n_neighbors = 30,
      dims = 2,
      verbose = FALSE,
      ...
    )

### Arguments

`object` | an CYT object
`umap.config` | object of class umap.config. See `umap`.
`n_neighbors` | numeric. Number of neighbors
`dims` | numeric. Dim of umap, you can also change it in umap.config.
`verbose` | logical. Whether to print calculation progress.
`...` | Options to pass on to the `umap` function

### Value

An CYT object

### See Also

`umap`

### Examples

    cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
    cyt <- readRDS(file = cyt.file)

    cyt <- runUMAP(cyt, verbose = TRUE)
    cyt <- runUMAP(cyt, n_neighbors = 20, verbose = TRUE)

[Package CytoTree version 1.4.0 Index]