Example #1
0
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
Example #2
0
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
Example #4
0
def presence_absence(table: biom.Table) -> biom.Table:
    """ Convert feature table in-place to presence/absence data
    """
    table.pa(inplace=True)
    return table