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` | 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)

[Package CytoTree version 1.0.3 Index]