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.
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:
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.