R: Embed a graph into a UMAP, Uniform Manifold Approximation and...

embedGraphUmap {sccore} | R Documentation

## Embed a graph into a UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction, <https://github.com/lmcinnes/umap>, <doi:10.21105/joss.00861>

### Description

Embed a graph into a UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction, <https://github.com/lmcinnes/umap>, <doi:10.21105/joss.00861>

### Usage

    embedGraphUmap(
      graph,
      min.prob = 0.001,
      min.visited.verts = 1000,
      n.cores = 1,
      max.hitting.nn.num = 0,
      max.commute.nn.num = 0,
      min.prob.lower = 1e-07,
      n.neighbors = 40,
      n.epochs = 1000,
      spread = 15,
      min.dist = 0.001,
      return.all = FALSE,
      n.sgd.cores = n.cores,
      verbose = TRUE,
      ...
    )

### Arguments

`graph` | input igraph object
`min.prob` | numeric Minimum probability for proximity when calculating hitting time per neighbors (default=1e-3)
`min.visited.verts` | numeric Minimum number of vertices visted when calculating hitting time per neighbors (default=1000)
`n.cores` | numeric Number of cores to use (default=1)
`max.hitting.nn.num` | numeric Maximum adjacencies for calculating hitting time per neighbor, hitting_time_per_neighbors() (default=0)
`max.commute.nn.num` | numeric Maximum adjacencies for calculating commute time per neighbor, commute_time_per_node() (default=0)
`min.prob.lower` | numeric Probability threshold to continue iteration in depth first search hitting time, dfs_hitting_time() (default=1e-7)
`n.neighbors` | numeric Number of neighbors (default=40)
`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()
`return.all` | boolean If TRUE, return list(adj.info=adj.info, commute.times=commute.times, umap=umap). Otherwise, just return UMAP(default=FALSE)
`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_threads) See 'n_sgd_threads' in uwot::umap()
`verbose` | boolean Verbose output (default=TRUE)
`...` | Additional arguments passed to embedKnnGraph()

### Value

resulting UMAP embedding

[Package sccore version 1.0.1 Index]