R: Embed a k-nearest neighbor (kNN) graph within a UMAP. Used...

embedKnnGraph {sccore} | R Documentation

## Embed a k-nearest neighbor (kNN) graph within a UMAP. Used within embedGraphUmap(). Please see McInnes et al <doi:10.21105/joss.00861> for the UMAP description and implementation.

### Description

Embed a k-nearest neighbor (kNN) graph within a UMAP. Used within embedGraphUmap(). Please see McInnes et al <doi:10.21105/joss.00861> for the UMAP description and implementation.

### Usage

    embedKnnGraph(
      commute.times,
      n.neighbors,
      names = NULL,
      n.cores = 1,
      n.epochs = 1000,
      spread = 15,
      min.dist = 0.001,
      n.sgd.cores = n.cores,
      target.dims = 2,
      verbose = TRUE,
      ...
    )

### Arguments

`commute.times` | graph commute times from get_nearest_neighbors(). The definition of commute_time(u, v) is the expected time starting at u = to reach v and then return to u .
`n.neighbors` | numeric Number of neighbors
`names` | vector of names for UMAP rownames (default=NULL)
`n.cores` | numeric Number of cores to use (except during stochastic gradient descent) (default=1). See 'n_threads' in uwot::umap()
`n.epochs` | numeric Number of epochs to use during the optimization of the embedded coordinates (default=1000). See 'n_epochs' in uwot::umap()
`spread` | numeric The effective scale of embedded points (numeric default=15). See 'spread' in uwot::umap()
`min.dist` | numeric The effective minimum distance between embedded points (default=0.001). See 'min.dist' in uwot::umap()
`n.sgd.cores` | numeric Number of cores to use during stochastic gradient descent. If set to > 1, then results will not be reproducible, even if 'set.seed' is called with a fixed seed before running (default=n.cores) See 'n_sgd_threads' in uwot::umap()
`target.dims` | numeric Dimensions for 'n_components' in uwot::umap(n_components=target.dims) (default=2)
`verbose` | boolean Verbose output (default=TRUE)
`...` | arguments passed to uwot::umap()

### Value

resulting kNN graph embedding within a UMAP

[Package sccore version 1.0.1 Index]