phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
are you interested in adding a (tiny) new feature to phyloseq?
I needed something to track what tax_glom and merge_taxa are doing and implemented a small feature to allow for a function (mostly relevant for pasting together or counting) to be applied to the length>1 entries of the merged/agglomerated taxa.
I exposed the argument I implemented for merge_taxa only to tax_glom, not to any other of the relevant higher level functions (the only other relevant one would probably be tip_glom, I guess).
I left the default intact, so it should not break anything. I added the required documentation (via devtools::document()) and did my best to make sure that devtools::check() complains only about stuff that has nothing to do with my changes.
Hi Paul,
are you interested in adding a (tiny) new feature to phyloseq?
I needed something to track what
tax_glomandmerge_taxaare doing and implemented a small feature to allow for a function (mostly relevant for pasting together or counting) to be applied to the length>1 entries of the merged/agglomerated taxa.I exposed the argument I implemented for
merge_taxaonly totax_glom, not to any other of the relevant higher level functions (the only other relevant one would probably betip_glom, I guess).I left the default intact, so it should not break anything. I added the required documentation (via
devtools::document()) and did my best to make sure thatdevtools::check()complains only about stuff that has nothing to do with my changes.Feel free to pull or ignore!
All the best, Emanuel