_visualizer.py 文件源码

def beta_rarefaction(output_dir: str, table: biom.Table, metric: str,
                     sampling_depth: int, iterations: int=10,
                     phylogeny: skbio.TreeNode=None,
                     correlation_method: str='spearman',
                     color_scheme: str='BrBG') -> None:
    if metric in phylogenetic_metrics():
        if phylogeny is None:
            raise ValueError("A phylogenetic metric (%s) was requested, "
                             "but a phylogenetic tree was not provided. "
                             "Phylogeny must be provided when using a "
                             "phylogenetic diversity metric." % metric)
        beta_func = functools.partial(beta_phylogenetic, phylogeny=phylogeny)
    else:
        beta_func = beta

    distance_matrices = _get_multiple_rarefaction(
        beta_func, metric, iterations, table, sampling_depth)

    sm_df = skbio.stats.distance.pwmantel(
        distance_matrices, method=correlation_method, permutations=0,
        strict=True)
    sm = sm_df[['statistic']]  # Drop all other DF columns
    sm = sm.unstack(level=0)  # Reshape for seaborn

    test_statistics = {'spearman': "Spearman's rho", 'pearson': "Pearson's r"}
    ax = sns.heatmap(
        sm, cmap=color_scheme, vmin=-1.0, vmax=1.0, center=0.0, annot=False,
        square=True, xticklabels=False, yticklabels=False,
        cbar_kws={'ticks': [1, 0.5, 0, -0.5, -1],
                  'label': test_statistics[correlation_method]})
    ax.set(xlabel='Iteration', ylabel='Iteration',
           title='Mantel correlation between iterations')
    ax.get_figure().savefig(os.path.join(output_dir, 'heatmap.svg'))

    similarity_mtx_fp = os.path.join(output_dir,
                                     'rarefaction-iteration-correlation.tsv')
    sm_df.to_csv(similarity_mtx_fp, sep='\t')

    index_fp = os.path.join(TEMPLATES, 'beta_rarefaction_assets', 'index.html')
    q2templates.render(index_fp, output_dir)