figure.alpha_diversity.py 文件源码

def plot_alphadf(alphasdf, col_order, labeldict, metric='alpha'):
    """
    Plot faceted alpha diversity.

    Parameters
    ----------
    alphasdf : pandas DataFrame
        columns ['study', 'alpha', 'DiseaseState']
    col_order : list
        dataset IDs in the order they should be plotted
    labeldict : dict
        dictionary with {dataset: label}
    mteric : str
        alpha diversity metric, to use in labeling y axis

    Returns
    -------
    fig : Figure
    """
    sns.set_style('white')
    g = sns.FacetGrid(alphasdf, col='study', col_wrap=6,
                      col_order=col_order, sharex=False, sharey=False)
    g = g.map(sns.boxplot, "DiseaseState", "alpha")
    g = g.map(sns.stripplot, "DiseaseState", "alpha", split=True, jitter=True,
              size=5, linewidth=0.6)

    fig = plt.gcf()
    fig.set_size_inches(14.2, 9)

    # Fix y-axis gridlines
    axs = g.axes
    for i in range(len(axs)):
        ax = axs[i]
        yticks = ax.get_yticks()
        # If bottom limit is between 0 and 1 (i.e. not simpson)
        if not (yticks[0] < 1 and yticks[0] > 0):
            ax.set_ylim(floor(yticks[0]), floor(yticks[-1]))
        if yticks[0] < 0:
            ax.set_ylim(0, floor(yticks[-1]))

        yticks = ax.get_yticks()
        if (yticks[0] < 1 and yticks[0] > 0):
            ax.set_yticks(yticks[1::2])
        else:
            ax.set_yticks(yticks[::2])
            # Need some space on the y-axis for p-values
            ax.set_ylim(ax.get_ylim()[0], 1.2*ax.get_ylim()[1])
        # Update title
        oldtitle = ax.get_title()
        newtitle = labeldict[oldtitle.split('=')[1].strip()]
        ax.set_title(newtitle)

        # Update y label
        if i % 6 == 0:
            ax.set_ylabel(metric)

    plt.tight_layout()
    return fig