runDiffusionMap {CytoTree}R Documentation

Calculate diffusion map in CYT

Description

Calculate diffusion map in CYT

Usage

runDiffusionMap(
  object,
  sigma.use = NULL,
  distance = c("euclidean", "cosine", "rankcor"),
  k = 30,
  density.norm = TRUE,
  verbose = FALSE,
  ...
)

Arguments

object

an CYT object

sigma.use

numeric. Diffusion scale parameter of the Gaussian kernel. One of 'local', 'global', a numeric global sigma or a Sigmas object. When choosing 'global', a global sigma will be calculated using find_sigmas (See destiny). A larger sigma might be necessary if the eigenvalues can not be found because of a singularity in the matrix. See destiny.

distance

Distance measurement method applied to data or a distance matrix/dist. For the allowed values, see destiny

k

numeric. By default is 30. destiny can be used to specify k.

density.norm

logical. If TRUE, use density normalisation. See destiny

verbose

logical. Whether to print calculation progress.

...

options to pass on to the destiny.

Value

An CYT object

See Also

destiny

Examples


cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

cyt <- runDiffusionMap(cyt, verbose = TRUE)
[Package CytoTree version 1.2.0 Index]