Convert an Seurat object to a SpaCET object.
Arguments
- Seurat_obj
An Seurat object.
- platform
A character string indicating the platform, i.e., "Visium", "OldST", or "Slide-Seq". "OldST" is the early in situ capturing method from which "Visium" was developed.
- visiumPath
Path to the Space Ranger output folder (Optional). If setting, this function will retrieve more information from the raw output.
Examples
visiumPath <- file.path(system.file(package = "SpaCET"), "extdata/Visium_BC")
Seurat_obj <- Seurat::Load10X_Spatial(data.dir = visiumPath)
SpaCET_obj <- convert.Seurat(Seurat_obj, platform = "Visium", visiumPath=NULL)
SpaCET_obj <- SpaCET.quality.control(SpaCET_obj)
SpaCET.visualize.spatialFeature(SpaCET_obj, spatialType = "QualityControl", spatialFeatures = c("UMI","Gene"))