Run a Giotto workflow

Run basic or full Giotto analysis on a `giotto2` object. Seurat input is converted first with [SeuratToScopGiotto()].

Usage

RunGiottoWorkflow(
  x,
  steps = c("basic", "full"),
  group.by = NULL,
  return_seurat = inherits(x, "Seurat"),
  store_results = TRUE,
  tool_name = "Giotto",
  verbose = TRUE,
  seed = 11,
  ...
)

Arguments

x

A `giotto2` or Seurat object.

steps

`"basic"` runs preprocessing, PCA/UMAP, nearest-network clustering, and spatial network construction. `"full"` additionally runs spatial genes, spatial modules, optional cell proximity, and HMRF.

group.by

Metadata column used for cell proximity enrichment.

return_seurat

Whether to return a Seurat object when `x` is Seurat. If `FALSE`, returns the internal `giotto2` workflow object.

store_results

Whether to store the internal Giotto workflow object in `srt@tools[[tool_name]]` when returning Seurat.

tool_name

Name used to store the Giotto workflow object in `srt@tools`.

verbose

Whether to print progress messages.

seed

Random seed for reproducible Giotto calls.

...

Passed to [SeuratToScopGiotto()] when `x` is Seurat.

Value

A Seurat object by default for Seurat input, otherwise a `giotto2` workflow object.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
g <- structure(
  list(
    source = list(
      cells = colnames(spatial),
      features = rownames(spatial),
      coordinates = data.frame(
        cell_ID = colnames(spatial),
        sdimx = spatial$x,
        sdimy = spatial$y
      )
    ),
    results = list(
      cluster = list(
        table = data.frame(
          cluster = paste0("cluster_", (seq_len(ncol(spatial)) - 1) %% 3 + 1),
          row.names = colnames(spatial)
        )
      )
    ),
    active = "cluster"
  ),
  class = c("giotto2", "list")
)
GiottoPlot(g, plot_type = "cluster")


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
g <- RunGiottoWorkflow(
  spatial,
  steps = "basic",
  assay = "Spatial",
  layer = "counts",
  coord.cols = c("x", "y"),
  return_seurat = FALSE,
  verbose = FALSE
)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"