Python  ·  2019/02/11

matplotlibで棒グラフ間の有意差の描画をする

（著）山たー

 

とりあえずメモ。2群比較とかで有意差の描画をPythonでどうやるか調べていたら、いい関数の実装を見つけた。

（参考）Indicating the statistically significant difference in bar graph

 

コード

from scipy import stats
import numpy as np
import matplotlib.pyplot as plt

np.random.seed(0)

def barplot_annotate_brackets(num1, num2, data, center, 
                              height, yerr=None, dh=.05, 
                              barh=.05, fs=None, maxasterix=None):
    """ 
    Annotate barplot with p-values.
 
    :param num1: number of left bar to put bracket over
    :param num2: number of right bar to put bracket over
    :param data: string to write or number for generating asterixes
    :param center: centers of all bars (like plt.bar() input)
    :param height: heights of all bars (like plt.bar() input)
    :param yerr: yerrs of all bars (like plt.bar() input)
    :param dh: height offset over bar / bar + yerr in axes coordinates (0 to 1)
    :param barh: bar height in axes coordinates (0 to 1)
    :param fs: font size
    :param maxasterix: maximum number of asterixes to write (for very small p-values)
    """
 
    if type(data) is str:
        text = data
    else:
        # * is p < 0.05
        # ** is p < 0.005
        # *** is p < 0.0005
        # etc.
        text = ''
        p = .05
 
        while data < p:
            text += '*'
            p /= 10.
 
            if maxasterix and len(text) == maxasterix:
                break
 
        if len(text) == 0:
            text = 'n. s.'
 
    lx, ly = center[num1], height[num1]
    rx, ry = center[num2], height[num2]
 
    if yerr:
        ly += yerr[num1]
        ry += yerr[num2]
 
    ax_y0, ax_y1 = plt.gca().get_ylim()
    dh *= (ax_y1 - ax_y0)
    barh *= (ax_y1 - ax_y0)
 
    y = max(ly, ry) + dh
 
    barx = [lx, lx, rx, rx]
    bary = [y, y+barh, y+barh, y]
    mid = ((lx+rx)/2, y+barh)
 
    plt.plot(barx, bary, c='black')
 
    kwargs = dict(ha='center', va='bottom')
    if fs is not None:
        kwargs['fontsize'] = fs
 
    plt.text(*mid, text, **kwargs)
     
""" main """
# Generate toy data
x0 = np.random.normal(loc=1.9, scale=0.4, size=100)
x1 = np.random.normal(loc=2, scale=0.3, size=100)
x2 = np.random.normal(loc=2.5, scale=0.8, size=50)

# Welch’s t-test
t01_value, p01_value = stats.ttest_ind(x0, x1, equal_var=False)
t02_value, p02_value = stats.ttest_ind(x0, x2, equal_var=False)
t12_value, p12_value = stats.ttest_ind(x1, x2, equal_var=False)


""" plot """
heights = [np.mean(x0), np.mean(x1), np.mean(x2)]
std = [np.std(x0), np.std(x1), np.std(x2)]
label = ["x0", "x1", "x2"]
width = 0.8 # the width of the bars
bars = np.arange(len(heights))
 
plt.figure(figsize=(4, 5))
plt.bar(bars, heights, width, tick_label=label, yerr=std,
        align='center', alpha=0.5, ecolor='black', capsize=5)
plt.ylim(0, 5)
barplot_annotate_brackets(0, 1, p01_value, bars,
                          heights, yerr=std)
barplot_annotate_brackets(0, 2, 'p < 0.001', bars,
                          heights, yerr=std)
barplot_annotate_brackets(1, 2, p12_value, bars,
                          heights, yerr=std,dh=0.2)
plt.tight_layout()
plt.savefig("barplot_sig.png")
plt.show()

他に参考にしたサイト

・https://matplotlib.org/examples/api/barchart_demo.html

 

コメントをお書きください

コメント: 5
  • #1

    LFOHP (水曜日, 10 6月 2020 08:42)

    とても興味あります。勉強になります、ありがとうございます。
    コードの理解が少し難しいです。個人的にでもおしえてもらえませんか？メールでもGitHubなどで各コードのコメントをつけてもらえませんか。

  • #2

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