[FIXED] Bland-Altman plot in Python

Issue

Is it possible to make a Bland-Altman plot in Python? I can't seem to find anything about it.

Another name for this type of plot is the Tukey mean-difference plot.

Example:

Solution

If I have understood the theory behind the plot correctly, this code should provide the basic plotting, whereas you can configure it to your own particular needs.

import matplotlib.pyplot as plt
import numpy as np

def bland_altman_plot(data1, data2, *args, **kwargs):
    data1     = np.asarray(data1)
    data2     = np.asarray(data2)
    mean      = np.mean([data1, data2], axis=0)
    diff      = data1 - data2                   # Difference between data1 and data2
    md        = np.mean(diff)                   # Mean of the difference
    sd        = np.std(diff, axis=0)            # Standard deviation of the difference

    plt.scatter(mean, diff, *args, **kwargs)
    plt.axhline(md,           color='gray', linestyle='--')
    plt.axhline(md + 1.96*sd, color='gray', linestyle='--')
    plt.axhline(md - 1.96*sd, color='gray', linestyle='--')

The corresponding elements in data1 and data2 are used to calculate the coordinates for the plotted points.

Then you can create a plot by running e.g.

from numpy.random import random

bland_altman_plot(random(10), random(10))
plt.title('Bland-Altman Plot')
plt.show()

Answered By - sodd