Seurat 5.1.0 Compatibility Issues

[LitingKu]

Hi there,

Thank you for develop SpaTalk!
I have tried to run the tutorial:

> library(SpaTalk)
> # load starmap data
> load(paste0(system.file(package = 'SpaTalk'), "/extdata/starmap_data.rda"))
> load(paste0(system.file(package = 'SpaTalk'), "/extdata/starmap_meta.rda"))
> # create SpaTalk data
> obj <- createSpaTalk(st_data = as.matrix(starmap_data),
+                      st_meta = starmap_meta[, -4],
+                      species = "Mouse",
+                      if_st_is_sc = T,
+                      spot_max_cell = 1)
> # decode the cell-type composition
> obj <- dec_celltype(object = obj,
+                     sc_data = as.matrix(starmap_data),
+                     sc_celltype = starmap_meta$celltype)
Error in .normalize_data(st_data) : 
  no slot of name "data" for this object of class "Assay5"
> packageVersion("Seurat")
[1] ‘5.1.0’
> 

But I found that the issue which has been closed seems still not fix #40

[multitalk]

Thanks for your feedback. I can run successfully locally based on the previous version. I have checked and updated the code in .normalize_data and re-run the tutorial successfully. You can try it again based on the newest version.

* DONE (SpaTalk)
> library(SpaTalk)
载入需要的程序包：ggalluvial
载入需要的程序包：ggplot2
载入需要的程序包：doParallel
载入需要的程序包：foreach
载入需要的程序包：iterators
载入需要的程序包：parallel
> load(paste0(system.file(package = 'SpaTalk'), "/extdata/starmap_data.rda"))
> load(paste0(system.file(package = 'SpaTalk'), "/extdata/starmap_meta.rda"))
> obj <- createSpaTalk(st_data = as.matrix(starmap_data), st_meta = starmap_meta[, -4], species = "Mouse", if_st_is_sc = T, spot_max_cell = 1)
> obj <- dec_celltype(object = obj, sc_data = as.matrix(starmap_data), sc_celltype = starmap_meta$celltype)
Performing Non-negative regression for each cell 
***Done*** 
> packageVersion("Seurat")
[1] ‘5.1.0’