def _read_inputs(biom_table: biom.Table, phylogeny_fp: NewickFormat,
meta_data: NumericMetadataColumn = None):
if meta_data:
generate_strategy = "balancing"
meta, biom_table = _sort_metada(meta_data, biom_table)
y = meta.iloc[:, 0]
samples = meta.index
else:
generate_strategy = "augmentation"
y = pd.Series(data=np.ones((len(biom_table.ids('sample')),)),
index=biom_table.ids('sample'))
samples = biom_table.ids('sample')
_table_tmp = biom_table.sort_order(axis='sample', order=samples)
_table = _map_observations(_table_tmp)
pruned_phylogeny_fp = _prune_features_from_phylogeny(_table, phylogeny_fp)
_tree = dendropy.Tree.get(path=str(pruned_phylogeny_fp),
preserve_underscores=False,
schema="newick", rooting='default-rooted')
if sum(samples != _table.ids('sample')) > 0:
raise ValueError("The samples IDs in meta data and biom table are "
"not the same! The difference is:",
set(samples) - set(_table.ids('sample')),
"Please double check.")
return _table, y, _tree, generate_strategy, pruned_phylogeny_fp
def plot(output_dir,
table: biom.Table,
metadata: q2.Metadata,
case_where: str,
control_where: str,
feature_tree: skbio.TreeNode = None):
with open('/tmp/tree.nwk', 'w') as fh:
feature_tree.write(fh)
copy_tree(os.path.join(PLOT, 'assets', 'dist'), output_dir)
data_dir = os.path.join(output_dir, 'data')
os.mkdir(data_dir)
metadata = metadata.filter_ids(table.ids(axis='sample'))
case_samples = sorted(list(metadata.get_ids(case_where)))
control_samples = sorted(list(metadata.get_ids(control_where)))
table.filter(case_samples + control_samples)
table.remove_empty('observation')
features = list(table.ids(axis='observation'))
if feature_tree is not None:
feature_tree = shear_no_prune(feature_tree, features)
else:
feature_tree = TreeNode()
tree_data = tree_to_array(feature_tree)
idx, = np.where(np.asarray(tree_data['children']) == 0)
tree_data['lookup'] = dict(zip(map(str, idx), range(len(idx))))
tip_order = np.asarray(tree_data['names'])[idx]
table = table.sort_order(tip_order, axis='observation')
table = table.sort_order(case_samples + control_samples, axis='sample')
with open(os.path.join(data_dir, 'packed_table.jsonp'), 'w') as fh:
fh.write('LOAD_PACKED_TABLE(')
fh.write(json.dumps(table_to_b64pa(table)))
fh.write(');')
with open(os.path.join(data_dir, 'tree.jsonp'), 'w') as fh:
fh.write('LOAD_TREE(')
fh.write(json.dumps(tree_data))
fh.write(');')
def _read_inputs(biom_table: biom.Table,
meta_data: NumericMetadataColumn = None):
if meta_data:
meta, biom_table = _sort_metada(meta_data, biom_table)
y = meta.iloc[:, 0]
samples = meta.index
else:
samples = biom_table.ids('sample')
y = pd.DataFrame(data=np.asarray(np.ones((len(samples), 1))).ravel(),
index=samples)
_table = biom_table.sort_order(axis='sample', order=samples)
if np.sum(samples != _table.ids('sample')) > 0:
raise ValueError(
"The samples IDs in meta data and biom table are not the same! The difference is:",
set(samples) - set(_table.ids('sample')), "Please double check.")
return _table, y
