Edward Zhao

Does the spec object have a `spatial.cluster` column? `spatialEnhance` defaults to using that column for initialization unless you have a different init vector of length equal to number of spots...

Hi Patricia, You can specify your color palette using the `palette` argument of `clusterPlot()`. The `init` parameter in `spatialEnhance()` allows you to set initial cluster assignments (at the spot level),...

hm, I'm not super sure what's going on here. Did you harmonize/integrate the PCs before running BayesSpace? Our [joint clustering vignette](https://edward130603.github.io/BayesSpace/articles/joint_clustering.html) goes through how to run BayesSpace across multiple samples...

Ok, I'm still not sure if I understand the problem. Are the clusters matching between your UMAP/SpatialDimPlots and your BayesSpace plots (and just the colors don't correspond)? Or is it...

I think the problem is right now, you are using the default initialization, and there is no guarantee these clusters will match up with those that you had in the...

Ok, so your sce right now has 1397 spots. It seems like `[email protected]` has length of 34170. Maybe need to subset `[email protected]` to only sample 1.15.

Yes, this is the relevant error message: ``` Error in [.data.frame(cdata, , c(x, y, "subspot.idx", fill)) : undefined columns selected ``` Can you check the column names of `sce1e`? I'm...

Can you both try plotting just your initialization using BayesSpace's `clusterPlot()` function? Does this match your Seurat plot? If not: - If the clusters are completely scrambled, check the order...

Unfortunately, we can't directly output character based cluster names at the moment, but if you know that "cluster 1" in your initialization maps to T cells, it should be straightforward...

I see you closed your other issue. Is this one still a problem? Can you give the output of `traceback()`? It seems like this error happens when you try to...