biocore/American-Gut — pull request #86 by wasade (2014-04-13 18:52:00+00:00)
Title: start of redo for phyla plots

A redo of the central logic for the phyla plots in module 2. This does not yet dump out graphics but the core logic should be in place.

An example to run:

``python phyla_plots.py -i ~/ag_fecal_even1k_L2.biom --samples 000004731.1076409,000010163.1213006 -m ~/AG_fecal_figure4.txt --categories AGE_CATEGORY,BMI_CATEGORY --n-most-common-taxa=8 > test_output.txt``

This optionally supports an identified sample. This code assumes the input table is a taxon table (eg the result of QIIME's ``summarize_taxa.py`` and assumes the table is in relative abundance.

@JWDebelius, can you please look through this code and see if it meshes? I _think_ this recreates the core logic of ``make_phyla_plots_AGP.py``. Any comments, or areas that need clarification, etc would be greatly appreciated. I'm pretty sure we can recycle the existing plotting code here, but I wanted to make sure the core logic was sound before we work on graphics. The debug output (which is forced to be enabled) can be opened in Excel and on spot checking, it seemed sane.

@adamrp and @ElDeveloper, when you have a chance, could you please comment on the code?