Run Giotto HMRF spatial domains

Usage

GiottoHMRF(
  x,
  spatial_genes = NULL,
  network_name = "Delaunay_full",
  k = 20,
  betas = c(0, 10, 20),
  hmrf_name = "scop_HMRF",
  params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

x: A `giotto2` workflow object.
spatial_genes: Spatial genes used by Giotto HMRF.
network_name: Name for the Giotto spatial network.
k: Number of HMRF domains.
betas: HMRF beta values.
hmrf_name: Name for the HMRF result.
params: Additional parameters passed to `Giotto::doHMRF()`.
verbose: Whether to print progress messages.
seed: Random seed for reproducible Giotto calls.

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)
)
hmrf_meta <- data.frame(
  cell_ID = colnames(spatial),
  scop_HMRF_k4_b10 = paste0("domain_", as.integer(factor(spatial$coda_label)) %% 4 + 1),
  row.names = colnames(spatial)
)
g <- structure(
  list(
    source = list(cells = colnames(spatial), coordinates = coords),
    results = list(
      hmrf = list(
        table = hmrf_meta["scop_HMRF_k4_b10"],
        metadata = hmrf_meta
      )
    )
  ),
  class = c("giotto2", "list")
)
GiottoPlot(g, plot_type = "hmrf")


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
  g <- SeuratToScopGiotto(spatial, coord.cols = c("x", "y"))
  g <- GiottoPreprocess(g)
  g <- GiottoSpatialNetwork(g)
  g <- GiottoHMRF(g, spatial_genes = rownames(spatial)[1:30], k = 4)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"