embedGraphUmap {sccore}

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