Subsetting from seurat object based on orig.ident?
If you are going to use idents like that, make sure that you have told the software what your default ident category is.
This works for me, with the metadata column being called &quot;group&quot;, and &quot;endo&quot; being one possible group there.
Idents(combined.all) &lt;- &quot;group&quot;
endo_subset &lt;- subset(combined.all, idents = c(&quot;endo&quot;))

I think this is basically what you did, but I think this looks a little nicer