Seurat5obj_to_SpaTopic: Convert a Seurat v5 object as the input of 'SpaTopic'

In SpaTopic: Topic Inference to Identify Tissue Architecture in Multiplexed Images

Convert a Seurat v5 object as the input of 'SpaTopic'

Description

Prepare 'SpaTopic' input from one Seurat v5 object

Usage

Seurat5obj_to_SpaTopic(object, group.by, image = "image1")

Arguments

object	Seurat v5 object
group.by	character. The name of the column that contains celltype information in the Seurat object.
image	character. The name of the image. Default is "image1".

Value

Return a data frame as the input of 'SpaTopic'

See Also

lung5

Examples

## nano.obj is a Seurat v5 object
#dataset<-Seurat5obj_to_SpaTopic(object = nano.obj, 
#                 group.by = "predicted.annotation.l1",image = "image1")
## Expect output
data("lung5")

SpaTopic documentation built on April 4, 2025, 1:38 a.m.