Run Giotto cell proximity enrichment

Usage

GiottoCellProximity(
  x,
  group.by,
  network_method = c("Delaunay", "kNN"),
  network_name = NULL,
  number_of_simulations = 1000,
  adjust_method = "fdr",
  params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

x: A `giotto2` workflow object.
group.by: Metadata column containing cell or spot groups.
network_method: Spatial network method.
network_name: Name for the Giotto spatial network.
number_of_simulations: Number of label simulations used by Giotto.
adjust_method: Multiple-testing correction method.
params: Additional parameters passed to `Giotto::cellProximityEnrichment()`.
verbose: Whether to print progress messages.
seed: Random seed for reproducible Giotto calls.

Value

A `giotto2` workflow object.

Examples

proximity <- data.frame(
  group_1 = c("Ductal", "Ductal", "Endocrine", "Stromal"),
  group_2 = c("Endocrine", "Stromal", "Stromal", "Ductal"),
  enrichment = c(1.6, 0.8, 1.3, 0.7),
  p.adj = c(0.01, 0.08, 0.03, 0.12)
)
g <- structure(
  list(
    results = list(cell_proximity = list(table = proximity)),
    parameters = list(network_method = "Delaunay", number_of_simulations = 100)
  ),
  class = c("giotto2", "list")
)
GiottoPlot(g, plot_type = "cell_proximity")


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
  data(visium_human_pancreas_sub)
  spatial <- visium_human_pancreas_sub
  g <- SeuratToScopGiotto(spatial, coord.cols = c("x", "y"))
  g <- GiottoSpatialNetwork(g)
  g <- GiottoCellProximity(g, group.by = "coda_label", number_of_simulations = 100)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"