TODO:

[mortonjt]

• Add more details about the balance_boxplot in the header: https://github.com/biocore/gneiss/blob/master/gneiss/plot/_decompose.py#L18 @lisa55asil

• Add more details about the proportion plot: https://github.com/biocore/gneiss/blob/master/gneiss/plot/_decompose.py#L82 @lisa55asil

• Make note of recursion stack limit in radialplot:
  Gneiss Maximum Recursion Depth Error #263
  https://github.com/biocore/gneiss/blob/master/gneiss/plot/_radial.py#L16 @lisa55asil

• Add docs for ilr transform (also specify that no zeros are allowed): https://github.com/biocore/gneiss/blob/master/gneiss/composition/_composition.py#L15 @lisa55asil

• Add links to patsy in q2 regression modules:
  http://patsy.readthedocs.io/en/latest/API-reference.html
  https://github.com/qiime2/q2-gneiss/blob/master/q2_gneiss/regression/_regression.py#L53
  https://github.com/qiime2/q2-gneiss/blob/master/q2_gneiss/regression/_regression.py#L93 @lisa55asil

• Update the newest docs. This will require updating the sphinx docs and pushing against master: Missing documentation for latest release #252 @lisa55asil

Bonus Features

• balance-taxonomy CSV header inconsistencies qiime2/q2-gneiss#26 (@kwcantrell)
• error if feature table samples aren't found in metadata qiime2/q2-gneiss#25 (@kwcantrell)
• Balance taxonomy colors are inconsistent  qiime2/q2-gneiss#27 (@kwcantrell)
• Create new methods ilr-transform-phylogenetic where the ilr transform returns both a tree and balancces. This will perform the bifurcate and rename_internal_nodes commands before returning the tree. This will be critical for enabling phylogenetic tree handling. Will require modifications to both here https://github.com/biocore/gneiss/blob/master/gneiss/composition/_composition.py#L15 and here https://github.com/qiime2/q2-gneiss/blob/master/q2_gneiss/composition/_composition.py (@qiyunzhu )
• In addition, merge an optional pseudocount parameter into ilr-transform, ilr-transform-phylogenetic and correlation-clustering so we can remove the add-pseudocount option in q2-gneiss. See here for more details: https://github.com/qiime2/q2-gneiss/blob/master/q2_gneiss/plugin_setup.py (@qiyunzhu )