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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
)

Arguments

object

An object of class Seurat with Visium data

image_type

One of "tissue_lowres" or "tissue_hires", specifying what H&E image was loaded into the Seurat object. Only used for "VisiumV1" data.

verbose

Print messages

Value

A Seurat object compatible with semla

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.

VisiumV2

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.

The getting started tutorial applies also for VisiumV2 assays. If you are working with VisiumHD data however, we recommend loading the data using semla's own functions, as detailed in the VisiumHD tutorial.

Note also that when adapting the object from hexagonal grid VisiumV2 to semla's object structure, array coordinates are not available. Thus, some plotting methods will not work.

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/VisiumV2 data (depends on your Seurat version)
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)
} # }