Create a Giotto spatial network

Usage

GiottoSpatialNetwork(
  x,
  network_method = c("Delaunay", "kNN"),
  network_name = NULL,
  params = list(),
  verbose = TRUE
)

Arguments

x: A `giotto2` workflow object.
network_method: Spatial network method.
network_name: Name for the Giotto spatial network.
params: Additional parameters passed to `Giotto::createSpatialNetwork()`.
verbose: Whether to print progress messages.

Value

A `giotto2` workflow object.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
coords <- data.frame(
  cell_ID = colnames(spatial),
  sdimx = spatial$x,
  sdimy = spatial$y,
  row.names = colnames(spatial)
)
edges <- data.frame(
  from = colnames(spatial)[1:79],
  to = colnames(spatial)[2:80]
)
g <- structure(
  list(
    source = list(cells = colnames(spatial), coordinates = coords),
    results = list(spatial_network = list(name = "Delaunay_network", table = edges))
  ),
  class = c("giotto2", "list")
)
GiottoPlot(g, plot_type = "network")


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
  g <- SeuratToScopGiotto(spatial, coord.cols = c("x", "y"))
  g <- GiottoSpatialNetwork(g, network_method = "Delaunay")
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"