Run Giotto dimensional reduction

Usage

GiottoReduce(
  x,
  reduction = c("pca", "umap"),
  dims = 1:20,
  name = NULL,
  features = NULL,
  params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

x: A `giotto2` workflow object.
reduction: Dimensional reduction to run.
dims: Dimensions to use.
name: Name for the Giotto reduction.
features: Features used for the reduction.
params: Additional parameters passed to the Giotto reduction 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
embedding <- cbind(
  UMAP_1 = as.numeric(scale(spatial$x)),
  UMAP_2 = as.numeric(scale(spatial$y))
)
rownames(embedding) <- colnames(spatial)
g <- structure(
  list(
    giotto = list(umap = embedding),
    source = list(cells = colnames(spatial), features = rownames(spatial)),
    results = list(
      cluster = list(
        table = data.frame(
          cell = colnames(spatial),
          cluster = spatial$coda_label,
          row.names = colnames(spatial)
        )
      )
    ),
    parameters = list(umap_name = "umap")
  ),
  class = c("giotto2", "list")
)
GiottoPlot(g, plot_type = "dim")


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 <- GiottoReduce(g, reduction = "umap", dims = 1:10)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"