Update a Seurat object for compatibility with semla
UpdateSeuratForSemla.Rd
In order to make a Seurat
object with semla
,
you can use AddSemlaToSeurat
to add the required
data to the Seurat
object. This assumes that
the Seurat
object contains one or more "VisiumV1"
object(s) in the images
slot. Alternatively, you
can convert a Seurat
object with "SlideSeq" data.
Usage
UpdateSeuratForSemla(
object,
image_type = c("tissue_lowres", "tissue_hires"),
verbose = TRUE
)
VisiumV1
Note that you need to specify what H&E image was loaded, one of "tissue_lowres" or "tissue_hires". If this argument is incorrect, the tissue coordinates will be misplaced.
Visit the getting started
tutorial on our package website for an example on how to convert a Seurat
object with
VisiumV1 data.
SlideSeq
For SlideSeq data, there's no additional H&E image provided. If you convert
a Seurat object containing SlideSeq data, all image related functionality
of semla
will be inaccessible.
Examples
if (FALSE) { # \dontrun{
library(semla)
library(SeuratData)
# Load example Seurat object with VisiumV1 data
InstallData("stxBrain")
brain <- LoadData("stxBrain", type = "anterior1")
# Make Seurat object compatible with semla
brain_semla <- UpdateSeuratForSemla(brain)
# Load example Seurat object with SlideSeq data
InstallData("ssHippo")
slide_seq <- LoadData("ssHippo")
# Make Seurat object compatible with semla
slide_seq <- UpdateSeuratForSemla(slide_seq)
} # }