Update the phyloseq_to_* functions.

vallenderlab / MicrobiomeR

A comprehensive and customizable R package for microbiome analysis.

https://vallenderlab.github.io/MicrobiomeR/

MIT License

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Update the phyloseq_to_* functions. #2

Closed grabear closed 5 years ago

grabear commented 6 years ago

The phyloseqto* functions need a few updates:

They need to have Stress/Control removed from syntax. Make dynamic for other users.
They need to consider rank for agglomerated phyloseq objects
For correlation plots, 2 ranks need to be sorted by significance.
- The legend order (super_rank) is currently based on p_values for the points (rank).
Update the phylsoeq_to_excelfunction to take a dataframe and list of column names.

grabear commented 6 years ago

Specifically phyloseq_to_excel() uses "rank" as a parameter. This was implemented only because get_correlation_plot() uses phyloseq::tax_glom() to study the data.

So ALL of the functions needed to be updated based on this

grabear commented 5 years ago

These functions are no longer relevant. Instead of using phyloseq objects for the data analysis, we are using metacoder for the data analysis. Phyloseq is now being suggested as the primary (but not only) means of importing data into R.