runUMAP {CytoTree} | R Documentation |
Calculate Uniform Manifold Approximation and Projection in CYT
runUMAP( object, umap.config = umap.defaults, n_neighbors = 30, dims = 2, verbose = FALSE, ... )
object |
a CYT object |
umap.config |
object of class umap.config. See |
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 |
A CYT object
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)