def observed_features(table: biom.Table) -> pd.Series:
presence_absence_table = table.pa(inplace=False)
counts = presence_absence_table.matrix_data.toarray().astype(int).T
sample_ids = presence_absence_table.ids(axis='sample')
result = skbio.diversity.alpha_diversity(metric='observed_otus',
counts=counts, ids=sample_ids)
result.name = 'observed_features'
return result
def faith_pd(table: biom.Table, phylogeny: skbio.TreeNode) -> pd.Series:
presence_absence_table = table.pa()
counts = presence_absence_table.matrix_data.toarray().astype(int).T
sample_ids = presence_absence_table.ids(axis='sample')
feature_ids = presence_absence_table.ids(axis='observation')
try:
result = skbio.diversity.alpha_diversity(metric='faith_pd',
counts=counts,
ids=sample_ids,
otu_ids=feature_ids,
tree=phylogeny)
except skbio.tree.MissingNodeError as e:
message = str(e).replace('otu_ids', 'feature_ids')
message = message.replace('tree', 'phylogeny')
raise skbio.tree.MissingNodeError(message)
result.name = 'faith_pd'
return result
def presence_absence(table: biom.Table) -> biom.Table:
""" Convert feature table in-place to presence/absence data
"""
table.pa(inplace=True)
return table
def presence_absence(table: biom.Table) -> biom.Table:
""" Convert feature table in-place to presence/absence data
"""
table.pa(inplace=True)
return table