run_umap: Run UMAP dimensionality reduction
In igordot/phenomenalist: Analysis Toolkit for PhenoCycler (CODEX) Data in R

run_umap

R Documentation

Run UMAP dimensionality reduction

Run UMAP dimensionality reduction

run_umap(
  x,
  assay = "exprs",
  n_neighbors = 50,
  min_dist = 0.01,
  n_threads = NULL,
  out_dir = NULL
)

`x`	A SpatialExperiment object.
`assay`	.
`n_neighbors`	The size of local neighborhood (in terms of number of neighboring sample points) used for manifold approximation. Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range `2` to `100`.
`min_dist`	The effective minimum distance between embedded points. Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the `spread` value, which determines the scale at which embedded points will be spread out.
`n_threads`	Number of threads to use (except during stochastic gradient descent). Default is half the number of concurrent threads supported by the system. For nearest neighbor search, only applies if `nn_method = "annoy"`. If `n_threads > 1`, then the Annoy index will be temporarily written to disk in the location determined by `tempfile`.
`out_dir`	Name of the output analysis directory. If specified, the object will be saved there.