search

AllenInstitute / scrattch.taxonomy

Allen Institute Taxonomy building R package
1 stars 1 forks source link

Adding customized dendrogram in buildPatchseqTaxonomy() #15

Open xuehanci opened 5 months ago

xuehanci commented 5 months ago

buildTaxonomy() is able to take in the existing dendrogram associated with the taxonomy, but buildPatchseqTaxonomy() doesn’t have this feature. It would be helpful to add a feature in buildPatchseqTaxonomy() to take in an existing patcheq dendrogram as well.

In the previous code that used the tree-mapping method for the mouse VISp taxonomy, a consolidated/collapsed dendrogram (where a branch could have more than two children) was used, which at the time improved mapping performance. For consistency with the past work, it would be good to be able to use the same dendrogram for that kind of mapping.

We could also have checks to ensure that the collapsed dendrogram given as input has a structure consistent with the original dendrogram and that it includes all the expected types.

UCDNJJ commented 5 months ago

I think this is a great addition, would you be up for implementing these changes under the recent updates?

xuehanci commented 5 months ago

I think this is a great addition, would you be up for implementing these changes under the recent updates?

Yes, I would be up to do so.