[ ] 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 )
[ ] 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: https://github.com/biocore/gneiss/issues/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: https://github.com/biocore/gneiss/issues/252 @lisa55asil
Bonus Features