How to combine spatial data from cell segmentation output with merge function

[AliceL90]

Hi All,

I have multiple Visium HD samples. I have generated seurat objects using the cell segmentation output from spaceranger. I would like to merge them all together. I have created a list of seurat objects and then I have applied the merge() function.
This is my code:

# List all .rds files
rds_files <- list.files(path, pattern = "\\cell_2um.rds$", full.names = TRUE)

# Read all Seurat objects
seu_list <- lapply(rds_files, readRDS)
clean_names <- tools::file_path_sans_ext(basename(seu_list))
clean_names <- sub("_cell_2um$", "", clean_names)
names(seu_list) <- clean_names

filename <- names(seu_list)

for (i in seq_along(seu_list)) {
  #i=1
  file <- seu_list[[i]]
  name <- names(seu_list[i])
  
  seu_list[[i]]@meta.data$orig.ident <- name
  Idents(file) <- "orig.ident"
  DefaultAssay(seu_list[[i]]) <- "Spatial.Polygons"
}

# Merge all objects
merged <- merge(seu_list[[1]], y = list(seu_list[[2]], seu_list[[3]], seu_list[[5]], seu_list[[7]],
                                        seu_list[[8]], seu_list[[9]], seu_list[[10]]), add.cell.ids = c("A", "B", "C", "D", "E", 
                                                                                                            "F", "G", "H"))

I get this error:

Error in FUN(): ! xmust be a vector, not a <sfc_POLYGON/sfc> object. Runrlang::last_trace() to see where the error occurred.

Is there any way to run merge on the Spatial.Polygons assay without encountering this error?

Many thanks for your help!

[QianhuiWan]

Hi Alice,

This works for me:

merge_seurats <- function(seurat_list) {
  stopifnot(length(seurat_list) >= 1)
  # add uniq id to spots
  for (i in seq_along(seurat_list)) {
    nm <- names(seurat_list)[i] %||% paste0("sample", i)
    names(seurat_list[[i]]@images) <- nm
  }
  if (length(seurat_list) == 1) return(seurat_list[[1]])
  merge(
    x = seurat_list[[1]],
    y = seurat_list[-1],
    add.cell.ids = names(seurat_list)
  )
}

# merge all objs, one obj per sample
obj_all <- merge_seurats(seurat_list = objs_list)

Best regards,
Qianhui