Estimate spot spacing from nearest-neighbor distances

Estimates the typical spacing between spots by computing each spot's nearest-neighbor distance (excluding itself) and returning the median of those distances. For large datasets, the estimate is computed on a random subsample for speed.

Usage

estimate_spot_spacing(df, sample_n = 1000)

Arguments

df

A data frame containing at least columns `x` and `y` (numeric) representing spot coordinates.

sample_n

Integer; maximum number of spots to sample (default `1000`). If `nrow(df) > sample_n`, a random subset of size `sample_n` is used; otherwise all spots are used.

Value

A numeric scalar: the median nearest-neighbor distance (in the same units as `x` and `y`).

Details

Nearest neighbors are computed with RANN::nn2() using `k = 2`. The first neighbor is the point itself (distance 0), so the function uses the second neighbor distance `nn$nn.dists[, 2]` as the true nearest-neighbor distance.

Missing values are handled via `median(..., na.rm = TRUE)`.

Examples

set.seed(1)
df <- data.frame(
  x = rep(1:5, each = 5),
  y = rep(1:5, times = 5)
)
estimate_spot_spacing(df)
#> [1] 1