runDiffusionMap: Calculate diffusion map in CYT

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

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	a 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

A 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)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.