Error: ! The slot argument of GetAssayData() was deprecated in SeuratObject 5.0.0 and is now defunct

[jiahaoliu-ai1]

When I run the code:
seurat_obj <- MetacellsByGroups(
seurat_obj = seurat_obj,assay="RNA",slot="counts",layer="counts",
group.by = c("celltype", "orig.ident"), # specify the columns in seurat_obj@meta.data to group by
reduction = 'pca', # select the dimensionality reduction to perform KNN on
k = 25, # nearest-neighbors parameter
max_shared = 10, # maximum number of shared cells between two metacells
ident.group = 'celltype' # set the Idents of the metacell seurat object
)

It tells me the error:
Error:

! The slot argument of GetAssayData() was deprecated in SeuratObject 5.0.0 and is now defunct.

ℹ Please use the layer argument instead.

Run rlang::last_trace() to see where the error occurred.

I've tried to join layers but useless. I saw a post here:satijalab/seurat#10250
What should I do currently to proceed?

[smorabit]

Hi @jiahaoliu-ai1 ,

Thanks for taking the time to describe your issue. Up until now hdWGCNA has worked with Seurat using either the old slot parameter from Seurat v4 and older, or the new layer parameter in Seurat v5 and up. However, it seems that in a recent Seurat update, slot no longer works. I will start working on an update to hdWGCNA.

At this time I am not sure exactly which version of Seurat or SeuratObject is causing the error. Can you please tell me which version you have?

packageVersion("Seurat")
packageVersion("SeuratObject")
packageVersion("hdWGCNA")

[jiahaoliu-ai1]

packageVersion("Seurat")
packageVersion("SeuratObject")
packageVersion("hdWGCNA")
[1] ‘5.4.0’
[1] ‘5.3.0’
[1] ‘0.4.8’

I used gemini to help me debug, it seemed that after deleting the code in MetacellsByGroups function, then it will not output error anymore.

if(!(slot %in% c('counts', 'data', 'scale.data'))){
stop('Invalid input for slot. Valid choices are counts, data, scale.data.')
} else{

# check the shape of the slot
slot_dim <- dim(Seurat::GetAssayData(seurat_obj, assay=assay, slot=slot))
if(any(slot_dim) == 0){
  stop(paste(c("Selected slot ", slot, " not found in this assay.")))
}

}

[Arch1baldL]

Similar issue appeared to me, when I ran:

seu.obj <- MetacellsByGroups(
    seurat_obj = seu.obj,
    group.by = c("cell_cluster", "orig.ident"),
    reduction = "harmony",
    k = 25,
    max_shared = 10,
    ident.group = "cell_cluster",
    min_cells = 50,
    assay = "RNA",
    slot = "counts"
)

With the version:

> packageVersion("Seurat")
[1] ‘5.3.1’
> packageVersion("SeuratObject")
[1] ‘5.3.0’
> packageVersion("hdWGCNA")
[1] ‘0.4.8’

Here is a temporary workaround that I fix it manually every time the package is loaded:

1. Activate Editor Mode

trace(hdWGCNA::MetacellsByGroups, edit = TRUE)

2. Searchfor GetAssayData (about line 35) and change the slot = slot to layer = slot

3. ESC and :wq

Hope that would help

[adairama]

Same issue here. I believe since Seurat version 5.4.0, if you use slot in GetAssayData, you get an error message instead of warning. This breaks several functions in other packages too. For me, I had to edit the MetacellsByGroups and ConstructMetacells function.