Run Giotto nearest-network clustering

Usage

GiottoCluster(
  x,
  method = c("leiden", "louvain"),
  dims = 1:20,
  k = 20,
  resolution = 1,
  network_name = "scop_NN",
  cluster_name = NULL,
  params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

x: A `giotto2` workflow object.
method: Giotto clustering method.
dims: Dimensions used to build the nearest-neighbor network.
k: Number of nearest neighbors.
resolution: Clustering resolution.
network_name: Name for the Giotto nearest-neighbor network.
cluster_name: Name for the Giotto cluster result.
params: Additional parameters passed to the Giotto clustering function.
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)
)
g <- structure(
  list(
    source = list(cells = colnames(spatial), coordinates = coords),
    results = list(
      cluster = list(
        table = data.frame(
          cell = colnames(spatial),
          cluster = spatial$coda_label,
          row.names = colnames(spatial)
        )
      )
    ),
    parameters = list(k = 8, resolution = 0.4)
  ),
  class = c("giotto2", "list")
)
GiottoPlot(g, plot_type = "cluster")


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
  g <- SeuratToScopGiotto(spatial, coord.cols = c("x", "y"))
  g <- GiottoPreprocess(g)
  g <- GiottoReduce(g, reduction = "pca", dims = 1:10)
  g <- GiottoCluster(g, dims = 1:10, k = 8, resolution = 0.4)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"