Scan cellular neighbourhoods.

Scan cellular neighbourhoods.

Usage

scanHoods(
  m,
  mode = c("proximityFocused", "smoothFadeout"),
  tau = NA,
  t_init = NA
)

Arguments

m

Distance matrix. Can be obtained from function findNearCells.

mode

Character. Either proximityFocused or smoothFadeout. By default is proximityFocused.

tau

The hyperparameter tau, by default is median(m**2)/5

t_init

An initial tau. In the smoothFadeout mode, user can provide an initial tau for optimization.

Value

A probability matrix.

Examples

m <- matrix(abs(rnorm(1000 * 100)), 1000, 100)

pm <- scanHoods(m)
#> Tau is set to: 0.0919819146408074