tax_glom add sample names

[g-antonello]

Dear Mike,
Thank you for this cool add-on, makes things so much faster. I have two suggestions:
(1) In the tax_glom function, you might add an option, that I suggest as default, which aggregates and renames taxa at that aggregation level, instead of leaving the unique OTU/ASV unique identifier. otherwise, I always have to do something like:

phy_genus <- tax_glom(physeq, "Genus")
taxa_names(phy_genus) <- taxa_names(phy_genus) <- tax_table(phy_genus)[,"Genus"]

I think it would simply mean adding this line to your function.

(2) I guess you thought about this already, but I was wondering if you could have a chat with joey711 to replace their functions with yours and improve the speed of phyloseq, because I think that most people use that package and don't know about this alternative.

[mikemc]

Hi @g-antonello, thanks for your comment. There is an important complication in that it cannot always be done, since for certain taxonomies like NCBI and Greengenes, a name is repeated for multiple taxa; e.g. there are multiple 'Clostridium' genera in these taxonomies. I would need to think about how to handle this; I could imagine having a command where that tells tax_glom to try to rename to the genus if possible, and if not to create a unique identifier e.g. "Family>Genus".

Realistically, I don't expect to address this myself soon, as I don't have time for active speedyseq development right now and I think the following is easy enough and has the benefit of making the renaming explicit,

phy_genus <- physeq %>%
  tax_glom("Genus") %>%
  mutate_tax_table(.otu = Genus)

I would consider a pull request (with good explanation and tests for the complicating factor noted above)

(2) I guess you thought about this already, but I was wondering if you could have a chat with joey711 to replace their functions with yours and improve the speed of phyloseq, because I think that most people use that package and don't know about this alternative.

I agree it would be good to incorporate the speed improvements directly into phyloseq so that everyone would benefit by default, but I posted about these some time ago without a response. My impression is that phyloseq is not under active maintenance and development anymore, so I don't expect this to happen anytime soon.

[g-antonello]

Dear Mike,
Thank you for your suggestions, I will think about suggesting a tweak in a more systematic way.
Giacomo