How to convert expression data and coordinate data in csv format to Seurat object for spatial transcriptomics analysis?

[YonghuiDong]

Hi all,

I am new to Seurat package. I want to convert two CSV files (expression data and coordinate data) into a Seurat object so that I could analyse the data in a manner like spatial transcriptomics (without optical or H&E image)

Here is my damo code:

library(Seurat)

#(1) Demo data
Expression <- data.frame(Cell1 = c(5.2, 1.5, 0), 
                         Cell2 = c(3.1, 0, 4.0), 
                         Cell3 = c(0, 2.2, 3.5)
                         )
rownames(Expression) <- c("GeneA", "GeneB", "GeneC")

Coord <- data.frame(CellID = c("Cell1", "Cell2", "Cell3"), 
                    x = c(12, 13, 11), 
                    y = c(34, 34, 35)
                    )

#(2) Create Seurat object
seurat_object <- CreateSeuratObject(counts = Expression)
seurat_object <- AddMetaData(seurat_object, metadata = Coord)

#(3) Plot 
SpatialPlot(seurat_object, features = "GeneA")

But I got the following error:

Could not find any spatial image information

Thanks a lot for your help.

Dong