Add Giotto results back to Seurat

Usage

AddGiottoToSeurat(
  srt,
  x,
  result = c("cluster", "hmrf"),
  name = NULL,
  tool_name = "Giotto",
  store_result = TRUE
)

Arguments

srt: A Seurat object.
x: A `giotto2` workflow object.
result: Giotto result to copy back.
name: Metadata column name to write. If `NULL`, a default name is used.
tool_name: Name used to store the Giotto workflow object in `srt@tools`.
store_result: Whether to store the Giotto workflow object in `srt@tools[[tool_name]]`.

Value

A Seurat object.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
g <- structure(
  list(
    source = list(cells = colnames(spatial)),
    results = list(
      cluster = list(
        table = data.frame(
          cell = colnames(spatial),
          cluster = spatial$coda_label,
          row.names = colnames(spatial)
        )
      )
    )
  ),
  class = c("giotto2", "list")
)
spatial <- AddGiottoToSeurat(
  spatial,
  g,
  result = "cluster",
  name = "Giotto_cluster",
  store_result = FALSE
)
SpatialSpotPlot(
  spatial,
  group.by = "Giotto_cluster",
  plot_type = "point",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)