Compatibility issue with SeuratObject 5.x: slot argument defunct in GetAssayData() #2
Description
Hi SpatialCellChat team,
I'm encountering a compatibility issue between SpatialCellChat and the latest SeuratObject 5.x. Here's the problem:
Environment
R version: 4.5
SeuratObject: 5.3.0
Seurat: 5.4.0
SpatialCellChat: latest version from GitHub
When running createSpatialCellChat() with SeuratObject 5.x, I get the following error:
chat <- createSpatialCellChat(
object = seu, # Seurat
group.by = "final.clusters",
assay = "Spatial", # normalized
datatype = "spatial",
coordinates = spatial.locs,
spatial.factors = spatial.factors
)
chat
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Traceback:
1. Seurat::GetAssayData(object, assay = assay, slot = "data")
2. GetAssayData.Seurat(object, assay = assay, slot = "data")
3. .Deprecate(when = "5.0.0", what = "GetAssayData(slot = )", with = "GetAssayData(layer = )")
4. deprecate_stop(when = wv, what = what, with = with, env = caller,
. ...)
5. deprecate_stop0(msg)
6. cnd_signal(error_cnd(c("lifecycle_error_deprecated", "defunctError"),
. old = NULL, new = NULL, package = NULL, message = msg))
7. signal_abort(cnd)
8. signalCondition(cnd)
Attempted Workaround
I tried downgrading SeuratObject to version 4.1.4 to avoid this issue. However, after downgrading, I cannot load SpatialCellChat at all:
Error: package or namespace load failed for 'SpatialCellChat':
object 'DefaultLayer<-' is not exported by 'namespace:SeuratObject'
Traceback:
1. tryCatch({
. attr(package, "LibPath") <- which.lib.loc
. ns <- loadNamespace(package, lib.loc)
. env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
. }, error = function(e) {
. P <- if (!is.null(cc <- conditionCall(e)))
. paste(" in", deparse(cc)[1L])
. else ""
. msg <- gettextf("package or namespace load failed for %s%s:\n %s",
. sQuote(package), P, conditionMessage(e))
. if (logical.return && !quietly)
. message(paste("Error:", msg), domain = NA)
. else stop(msg, call. = FALSE, domain = NA)
. })
2. tryCatchList(expr, classes, parentenv, handlers)
3. tryCatchOne(expr, names, parentenv, handlers[[1L]])
4. value[[3L]](cond)
5. stop(msg, call. = FALSE, domain = NA)
6. .handleSimpleError(function (cnd)
. {
. watcher$capture_plot_and_output()
. cnd <- sanitize_call(cnd)
. watcher$push(cnd)
. switch(on_error, continue = invokeRestart("eval_continue"),
. stop = invokeRestart("eval_stop"), error = NULL)
. }, "package or namespace load failed for 'SpatialCellChat':\n object 'DefaultLayer<-' is not exported by 'namespace:SeuratObject'",
. base::quote(NULL))
Could you please provide guidance on which version combination works currently?
Thank you for your help!