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AllenInstitute / scrattch.taxonomy

Allen Institute Taxonomy building R package
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Issue with addDendrogramMarkers() #17

Open xuehanci opened 6 months ago

xuehanci commented 6 months ago

In the example build_taxonomy.md, there is this step that adding markers to dendrogram for the parent taxonomy addDendrogramMarkers(). And then create the patchseq child taxonomy. However this step is giving me error after the recent changes with scrattch.taxonomy:

Error in AIT.anndata$uns$QC_markers[[mode]][["de_genes"]] <- de.genes : more elements supplied than there are to replace

I realized that addDendrogramMarkers() is also embedded within buildPatchseqTaxonomy(), if I don't run addDendrogramMarkers() after buildTaxonomy() and just run buildPatchseqTaxonomy(), it doesn't give me any error. (Steps in build_MTG_patchseq_taxonomy.md)

I am wondering if addDendrogramMarkers() is still needed after build_taxonomy().

UCDNJJ commented 6 months ago

I'll take a look into this, I was having the same error last week. Ideally you should be able to run addDendrogramMarkers at any point! Thanks for catching this error.