bland_altman_plot.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import numpy as np
from matplotlib import pyplot as plt
from matplotlib.transforms import blended_transform_factory


def bland_altman(x, y, axis=None, sd_offset=1.96,
                 n_format='{0:.2f}', *args, **kwargs):
    if not axis:
        axis = plt.gca()

    mean = np.mean([x, y], axis=0)
    diff = x - y
    md   = np.mean(diff)
    sd   = np.std(diff, axis=0)

    axis.scatter(mean, diff, *args, **kwargs)
    axis.axhline(md,                  linestyle='--', *args, **kwargs)
    axis.axhline(md + sd_offset * sd, linestyle='--', *args, **kwargs)
    axis.axhline(md - sd_offset * sd, linestyle='--', *args, **kwargs)

    tform = blended_transform_factory(axis.transAxes, axis.transData)
    axis.annotate('MEAN\n' + n_format.format(md), xy=(0, 0),
                  xycoords=tform, xytext=(0.98, md),
                  textcoords=tform, ha='right', va='center', *args, **kwargs)
    axis.annotate(('+%sSD\n' % sd_offset) + n_format.format(md + sd_offset * sd),
                  xy=(0, 0), xycoords=tform, xytext=(0.98, md + sd_offset * sd),
                  textcoords=tform, ha='right', va='center', *args, **kwargs)
    axis.annotate(('-%sSD\n' % sd_offset) + n_format.format(md - sd_offset * sd),
                  xy=(0, 0), xycoords=tform, xytext=(0.98, md - sd_offset * sd),
                  textcoords=tform, ha='right', va='center', *args, **kwargs)



if __name__ == "__main__":
    x = np.random.randn(100)
    y = np.random.randn(100)

    bland_altman(x, y, color='black')
    plt.show()