Convert Seurat to a native Giotto object — srt_to

Convert one Seurat spatial image into a native Giotto object without running a Giotto workflow or changing the input object.

Usage

srt_to_giotto(object, image = NULL, ..., srt = NULL)

Arguments

object: A `Seurat` object.
image: Seurat image name. Multi-image objects require an explicit name.
...: Additional arguments passed to the Giotto converter.
srt: Deprecated alias for `object`; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A native Giotto object.

Details

Converters live in GiottoClass. If that package is already installed from any source, the bridge reuses it and does not reinstall `drieslab/Giotto`. A GitHub reinstall is requested only when GiottoClass is missing. Conversion does not initialize Giotto's optional Python/conda environment.

Examples

if (FALSE) { # \dontrun{
data(visium_human_pancreas_sub)
spatial <- Seurat::NormalizeData(
  visium_human_pancreas_sub,
  assay = "Spatial",
  verbose = FALSE
)
giotto <- srt_to_giotto(spatial, image = "slice1")
print(giotto)
} # }