Build a native spatial network

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

Arguments

object

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.

sample.by

Optional metadata column identifying independent spatial samples. The selected image/coordinate nodes must belong to one non-missing sample. Subset independent samples and build their graphs separately; this guard does not split graphs. `NULL` retains existing behavior.

verbose

Whether to print the message. Default is TRUE.

srt

Deprecated alias for `object`; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

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

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- RunSpatialNetwork(object = spatial, k = 6, verbose = FALSE)
SpatialNetworkPlot(object = spatial, group.by = "coda_label")