def __init__(self,
table: biom.Table,
features: pd.DataFrame,
variances: biom.Table = None,
formatter: Optional['Formatter'] = None):
"""Establish the taxonomy data
Parameters
----------
table : biom.Table
Relative abundance data per sample or collapsed into higher order
entiries (e.g., abx in the past year)
features : pd.DataFrame
DataFrame relating an observation to a Taxon
variances : biom.Table, optional
Variation information about a taxon within a label.
"""
self._table = table.norm(inplace=False)
self._group_id_lookup = set(self._table.ids())
self._feature_id_lookup = set(self._table.ids(axis='observation'))
self._feature_order = self._table.ids(axis='observation')
self._features = features
self._ranks = table.rankdata(inplace=False)
if variances is None:
self._variances = biom.Table(np.zeros(self._table.shape),
self._table.ids(axis='observation'),
self._table.ids())
else:
self._variances = variances
if set(self._variances.ids()) != set(self._table.ids()):
raise DisjointError("Table and variances are disjoint")
if set(self._variances.ids(axis='observation')) != \
set(self._table.ids(axis='observation')):
raise DisjointError("Table and variances are disjoint")
if set(self._table.ids(axis='observation')) != \
set(self._features.index):
raise DisjointError("Table and features are disjoint")
self._features = self._features.loc[self._feature_order]
self._variances = self._variances.sort_order(self._feature_order,
axis='observation')
if formatter is None:
formatter: Formatter = GreengenesFormatter()
self._formatter = formatter
feature_taxons = self._features
self._formatted_taxa_names = {
i: self._formatter.dict_format(lineage)
for i, lineage in feature_taxons['Taxon'].items()
}
