Smooth spot-level SE abundances across k-nearest-neighbor spots
Source:R/ComputeSEAbundanceBySN.R
SmoothSEAbundances.RdSmooth spot-level SE abundances across k-nearest-neighbor spots
Usage
SmoothSEAbundances(
se_mat,
spot_coords,
k = 7,
X = "X",
Y = "Y",
include.self = TRUE,
min.neighbors = 3
)Arguments
- se_mat
spot x SE matrix (rownames = spot IDs), values indicating SE abundance/level in each Visium spot.
- spot_coords
data.frame/matrix of spot coordinates (rownames = spot IDs, must overlap with `rownames(se_mat)`), columns given by `X`, `Y`.
- k
number of nearest-neighbor spots to average over. Default 7, matching a Visium hex grid (1 self + 6 immediate neighbors) when `include.self = TRUE`.
- X, Y
column names in `spot_coords` for x/y coordinates.
- include.self
if TRUE (default), each spot's own value is included as one of its k neighbors (so k=7 = self + 6 hex neighbors). If FALSE, only the k nearest *other* spots are averaged.
- min.neighbors
minimum number of neighbor spots required to keep a spot in the output.