Sigmas-class {destiny} | R Documentation

## Sigmas Object

### Description

Holds the information about how the `sigma` parameter for a DiffusionMap was obtained, and in this way provides a plotting function for the find_sigmas heuristic. You should not need to create a Sigmas object yourself. Provide `sigma` to DiffusionMap instead or use find_sigmas.

### Usage

    Sigmas(...)

    ## S4 method for signature 'Sigmas'
    optimal_sigma(object)

    ## S4 method for signature 'Sigmas'
    print(x)

    ## S4 method for signature 'Sigmas'
    show(object)

### Arguments

`object, x` | Sigmas object
`...` | See “Slots” below

### Details

A Sigmas object is either created by find_sigmas or by specifying the `sigma` parameter to DiffusionMap.

In the second case, if the `sigma` parameter is just a number, the resulting `Sigmas` object has all slots except of `optimal_sigma` set to `NULL`.

### Value

`Sigmas` creates an object of the same class

`optimal_sigma` retrieves the numeric value of the optimal sigma or local sigmas

### Slots

`log_sigmas`

  Vector of length m containing the \log_{10} of the σs

`dim_norms`

  Vector of length m-1 containing the average dimensionality \langle p \rangle for the respective kernel widths

`optimal_sigma`

  Multiple local sigmas or the mean of the two global σs around the highest \langle p \rangle (`c(optimal_idx, optimal_idx+1L)`)

`optimal_idx`

  The index of the highest \langle p \rangle.

`avrd_norms`

  Vector of length m containing the average dimensionality for the corresponding sigma.

### See Also

`find_sigmas`, the function to determine a locally optimal sigma and returning this class

### Examples

    data(guo)
    sigs <- find_sigmas(guo, verbose = FALSE)
    optimal_sigma(sigs)
    print(sigs)

[Package destiny version 3.1.0 Index]