Preprocess an internal Giotto workflow object

Usage

GiottoPreprocess(
  x,
  filter_params = list(),
  norm_params = list(),
  stat_params = list(),
  hvf_params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

x: A `giotto2` workflow object.
filter_params: Additional parameters reserved for future filtering.
norm_params: Additional parameters passed to `Giotto::normalizeGiotto()`.
stat_params: Additional parameters passed to `Giotto::addStatistics()`.
hvf_params: Additional parameters passed to `Giotto::calculateHVF()`.
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
g <- structure(
  list(
    source = list(
      cells = colnames(spatial),
      features = rownames(spatial)[1:100],
      coordinates = data.frame(cell_ID = colnames(spatial), sdimx = spatial$x, sdimy = spatial$y)
    ),
    results = list(),
    active = NULL
  ),
  class = c("giotto2", "list")
)
GiottoPlot(g, plot_type = "spatial")


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