Build a native spatial network — RunSpatialNetwork • scop

Build a k-nearest-neighbor or radius spatial network from raw Seurat spatial coordinates. Results are stored as named graphs in `srt@tools$SpatialNetwork`.

Usage

RunSpatialNetwork(
  srt,
  method = c("knn", "radius"),
  image = NULL,
  coord.cols = c("col", "row"),
  k = 6,
  radius = NULL,
  graph.name = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

srt: A `Seurat` object.
method: Network method, either `"knn"` or `"radius"`.
image: Seurat image name. A single image is selected automatically; multi-image objects require an explicit value.
coord.cols: Metadata columns used when the object has no image.
k: Number of neighbors for `method = "knn"`.
radius: Positive distance threshold for `method = "radius"`, expressed in the raw coordinate units.
graph.name: Optional graph name. If `NULL`, a deterministic name is generated from the image, method, and method parameter.
overwrite: Whether an existing graph with the same name may be replaced.
verbose: Whether to print the message. Default is TRUE.

Value

The input `Seurat` object with a `SpatialNetwork` result in `srt@tools`.

Examples

counts <- matrix(
  c(3, 1, 0, 2, 0, 4, 1, 0, 2, 1, 3, 0),
  nrow = 3,
  dimnames = list(paste0("gene", 1:3), paste0("spot", 1:4))
)
srt <- SeuratObject::CreateSeuratObject(counts)
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
srt$col <- c(0, 1, 0, 1)
srt$row <- c(0, 0, 1, 1)
srt <- RunSpatialNetwork(srt, k = 2, verbose = FALSE)
SpatialNetworkPlot(srt)