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AllenInstitute / scrattch.taxonomy

Allen Institute Taxonomy building R package
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(Non-breaking) issues with loadTaxonomy and checkTaxonomy #11

Open jeremymiller opened 9 months ago

jeremymiller commented 9 months ago

loadTaxonomy issue I keep getting this error when taxonomies are being created from a docker. "Loading an older AIT .h5ad version. Converting dendrogram to JSON format for mapping." I suspect that it is not correctly looking for the JSON format in the uns before rewriting it from the .RDS file.

checkTaxonomy issues Even with a valid taxonomy, I get this issue "WARNING: A UMAP is invalid or not provided in AIT.anndata$obsm$umap." Probably some minor update needed. Also, I think it only checks "standard" and not the other modes (e.g., AIT30.1)

UCDNJJ commented 7 months ago

I handled the dendrogram message, essentially the print statement was in the wrong spot and typically didn't apply :).

UMAP is still unresolved.