Sigmas-class: Sigmas Object

In theislab/destiny: Creates diffusion maps

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 \sigmas

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 \sigmas 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)

theislab/destiny documentation built on Jan. 27, 2024, 9:57 p.m.