Read or convert a stored spatial graph

Read a graph from a `SpatialNetwork` result without modifying the Seurat object. Graphs can be returned as their complete list representation, a sparse matrix, or a Seurat `Graph` object.

Usage

GetSpatialGraph(
  object = NULL,
  res = NULL,
  graph.name = NULL,
  format = c("list", "sparse", "seurat"),
  value = c("weight", "distance")
)

Arguments

object

Optional `Seurat` object containing `SpatialNetwork` results.

res

Optional `SpatialNetwork` result list.

graph.name

Stored graph name. The active graph is used when `NULL`.

format

Output representation.

value

Edge value used for matrix conversions.

Value

A graph list, `dgCMatrix`, or Seurat `Graph` object.

Examples

data(visium_human_pancreas_sub)
spatial <- RunSpatialNetwork(
  visium_human_pancreas_sub,
  k = 6,
  coord.cols = c("x", "y"),
  verbose = FALSE
)
graph <- GetSpatialGraph(spatial, format = "list")
graph_sparse <- GetSpatialGraph(spatial, format = "sparse")
c(nodes = nrow(graph$nodes), edges = nrow(graph$edges))
#> nodes edges 
#>  1986  6358 
graph_sparse[
  seq_len(min(3, nrow(graph_sparse))),
  seq_len(min(3, ncol(graph_sparse)))
]
#> 3 x 3 sparse Matrix of class "dgCMatrix"
#>                    TGGTATCGGTCTGTAT-1 ATTATCTCGACAGATC-1 TGAGATCAAATACTCA-1
#> TGGTATCGGTCTGTAT-1                  .                  1                  .
#> ATTATCTCGACAGATC-1                  1                  .                  1
#> TGAGATCAAATACTCA-1                  .                  1                  .