tools.py 文件源码

def aga_attachedness(
        adata,
        attachedness_type='scaled',
        color_map=None,
        show=None,
        save=None):
    """Attachedness of aga groups.
    """
    if attachedness_type == 'scaled':
        attachedness = adata.uns['aga_attachedness']
    elif attachedness_type == 'distance':
        attachedness = adata.uns['aga_distances']
    elif attachedness_type == 'absolute':
        attachedness = adata.uns['aga_attachedness_absolute']
    else:
        raise ValueError('Unkown attachedness_type {}.'.format(attachedness_type))
    adjacency = adata.uns['aga_adjacency']
    matrix(attachedness, color_map=color_map, show=False)
    for i in range(adjacency.shape[0]):
        neighbors = adjacency[i].nonzero()[1]
        pl.scatter([i for j in neighbors], neighbors, color='green')
    utils.savefig_or_show('aga_attachedness', show=show, save=save)
    # as a stripplot
    if False:
        pl.figure()
        for i, ds in enumerate(attachedness):
            ds = np.log1p(ds)
            x = [i for j, d in enumerate(ds) if i != j]
            y = [d for j, d in enumerate(ds) if i != j]
            pl.scatter(x, y, color='gray')
            neighbors = adjacency[i]
            pl.scatter([i for j in neighbors],
                       ds[neighbors], color='green')
        pl.show()