Run Giotto cell proximity enrichment — RunGiottoCellProximity • scop

Use Giotto as a temporary backend to build a spatial network and test pairwise enrichment between metadata groups. The complete Giotto object and result tables are returned as a standalone result; the input Seurat object is not modified.

Usage

RunGiottoCellProximity(
  srt,
  group.by,
  assay = NULL,
  layer = "data",
  image = NULL,
  coord.cols = c("x", "y"),
  network_method = c("Delaunay", "kNN"),
  network_name = NULL,
  number_of_simulations = 1000,
  adjust_method = "fdr",
  tool_name = "GiottoCellProximity",
  store_giotto = TRUE,
  conversion_params = list(),
  network_params = list(),
  enrichment_params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

srt: A Seurat object.
group.by: Seurat metadata column containing cell or spot groups.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
layer: Assay layer used as the expression matrix.
image: Name of the Seurat spatial image used by the spatial workflow. If NULL, the first image is used when present.
coord.cols: Metadata coordinate columns used by the spatial workflow when no image is available.
network_method: Spatial network method passed to Giotto::createSpatialNetwork().
network_name: Name for the Giotto spatial network.
number_of_simulations: Number of label simulations used by Giotto.
adjust_method: Multiple-testing correction method.
tool_name: Result name recorded in returned parameters. This function does not write to srt@tools.
store_giotto: Deprecated compatibility argument. The complete Giotto object is always returned in the giotto element.
conversion_params: Additional parameters passed to Giotto::createGiottoObject().
network_params: Additional parameters passed to Giotto::createSpatialNetwork().
enrichment_params: Additional parameters passed to Giotto::cellProximityEnrichment().
verbose: Whether to print the message. Default is TRUE.
seed: Random seed for reproducibility. Default is 11.

Value

A giotto2_result list containing the full Giotto object, enrichment table, raw Giotto result, parameters, features, and cells.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial$region <- ifelse(
  spatial$x > stats::median(spatial$x),
  "right",
  "left"
)
proximity <- list(
  enrichment = data.frame(
    group_1 = c("left", "left", "right", "right"),
    group_2 = c("left", "right", "left", "right"),
    enrichment = c(1.1, -0.7, -0.5, 1.3),
    type_int = c("enriched", "depleted", "depleted", "enriched")
  ),
  parameters = list(network_method = "Delaunay", number_of_simulations = 100)
)
class(proximity) <- c("giotto2_cell_proximity", "giotto2_result", "list")

head(proximity$enrichment)
#>   group_1 group_2 enrichment type_int
#> 1    left    left        1.1 enriched
#> 2    left   right       -0.7 depleted
#> 3   right    left       -0.5 depleted
#> 4   right   right        1.3 enriched
GiottoPlot(proximity)


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)
proximity <- RunGiottoCellProximity(
  spatial,
  group.by = "region",
  assay = "Spatial",
  layer = "data",
  coord.cols = c("x", "y"),
  network_method = "Delaunay",
  number_of_simulations = 100
)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"