problem with Visium HD spatial transcripts data

[cmubioinformatics]

# Create grouped features grouped_features <- list( "B_cell_markers" = c("MS4A1", "CD79A"), "T_cell_markers" = c("CD3D", "CD8A", "IL7R"), "Myeloid_markers" = c("CD14", "FCGR3A", "S100A8") )

DotPlot2(stRNA, features = grouped_features)

`Error in match.arg(arg = value, choices = Assays(object = object)): 'arg' should be “Spatial”
Traceback:

1. feature_percent(seu, tp, group.by = calc_group.by)
2. DefaultAssay<-(*tmp*, value = DefaultAssay)
3. DefaultAssay<-.Seurat(*tmp*, value = DefaultAssay)
4. match.arg(arg = value, choices = Assays(object = object))
5. stop(sprintf(ngettext(length(chs <- unique(choices[nzchar(choices)])),
   . "'arg' should be %s", "'arg' should be one of %s"), paste(dQuote(chs),
   . collapse = ", ")), 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)
   . }, "'arg' should be “Spatial”", base::quote(match.arg(arg = value,
   . choices = Assays(object = object))))`

could you tell me how to solve this problem? thanks

[huayc09]

Thank you for your question. The DotPlot2 function has been tested with Xenium spatial data and works there, but I'm not as familiar with Visium HD data. I downloaded the official 10X Visium HD dataset to test, but I wasn't able to reproduce your exact error (though I did encounter a different error).

I'll need some more time to find the best adaptation solution for this issue. The error suggests there's a problem with the assay handling in the feature_percent function when working with Visium data, where it's expecting "Spatial" as the default assay but something else is being set.

Let me continue investigating this and I'll provide a solution as soon as I can.

[cmubioinformatics]

Thank you for your question. The DotPlot2 function has been tested with Xenium spatial data and works there, but I'm not as familiar with Visium HD data. I downloaded the official 10X Visium HD dataset to test, but I wasn't able to reproduce your exact error (though I did encounter a different error).

I'll need some more time to find the best adaptation solution for this issue. The error suggests there's a problem with the assay handling in the feature_percent function when working with Visium data, where it's expecting "Spatial" as the default assay but something else is being set.

Let me continue investigating this and I'll provide a solution as soon as I can.

good good, waiting for you honey