runDiffusionMap {CytoTree} | R Documentation |
Calculate diffusion map in CYT
runDiffusionMap( object, sigma.use = NULL, distance = c("euclidean", "cosine", "rankcor"), k = 30, density.norm = TRUE, verbose = FALSE, ... )
object |
a CYT object |
sigma.use |
numeric. Diffusion scale parameter of the Gaussian kernel.
One of ' |
distance |
Distance measurement method applied to data or a distance matrix/dist.
For the allowed values, see |
k |
numeric. By default is 30. |
density.norm |
logical. If TRUE, use density normalisation. See |
verbose |
logical. Whether to print calculation progress. |
... |
options to pass on to the |
A CYT object
destiny
cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree") cyt <- readRDS(file = cyt.file) cyt <- runDiffusionMap(cyt, verbose = TRUE)