phyloseq support

[davidvilanova]

Hello,
Would it be possible to have phyloseq support or an easy way of building a new gneiss object based on a phyloseq object.

Thanks

[mortonjt]

Hi @davidvilanova , that may require a substantial amount of work -- I can't currently envision near-term support for phyloseq compatibility.

There are two ways to currently go about this.

1. Download the newick files and resulting model parameters in the qiime2 plugin and parse out those results using ape or another R package for parsing trees. You can also export the results from the ilr-transform provided in qiime2 - and import those transformed values into R.

2. If you want to redo the ilr transform / statistical modeling to enable tightly coupled support with phyloseq, it maybe worth looking into the following packages. It should be possible, but will require a bit amount of software engineering to get the tree fully linked to the phyloseq objects.

https://github.com/jsilve24/philr
https://github.com/reptalex/phylofactor
https://cran.r-project.org/web/packages/compositions/index.html