CoCalc Shared Filesscikit-posthocs.ipynb
Author: Harald Schilly
Views : 83
Description: Pairwise Multiple Comparisons Post-hoc Tests

# scikit-posthocs

## Pairwise Multiple Comparisons Post-hoc Tests

in Python 3 (Ubuntu Linux)

https://github.com/maximtrp/scikit-posthocs

In [1]:
import scikit_posthocs as sp
x = [[1,2,3,5,1], [12,31,54], [10,12,6,74,11]]

array([[-1. , 0.00119517, 0.00278329], [ 0.00119517, -1. , 0.18672227], [ 0.00278329, 0.18672227, -1. ]])
In [2]:
import scikit_posthocs as sp
import pandas as pd
x = pd.DataFrame({"a": [1,2,3,5,1], "b": [12,31,54,62,12], "c": [10,12,6,74,11]})
x = x.melt(var_name='groups', value_name='values')
x

groups values
0 a 1
1 a 2
2 a 3
3 a 5
4 a 1
5 b 12
6 b 31
7 b 54
8 b 62
9 b 12
10 c 10
11 c 12
12 c 6
13 c 74
14 c 11
In [3]:
sp.posthoc_conover(x, val_col='values', group_col='groups')

a b c
a -1.000000 0.000109 0.001853
b 0.000109 -1.000000 0.121659
c 0.001853 0.121659 -1.000000
In [4]:
pc = sp.posthoc_conover(x, val_col='values', group_col='groups')
heatmap_args = {'linewidths': 0.25, 'linecolor': '0.5', 'clip_on': False, 'square': True, 'cbar_ax_bbox': [0.80, 0.35, 0.04, 0.3]}
sp.sign_plot(pc, **heatmap_args)

(<matplotlib.axes._subplots.AxesSubplot at 0x7f67b595ffd0>, <matplotlib.colorbar.ColorbarBase at 0x7f67b160c128>)
In [5]:
pc = sp.posthoc_conover(x, val_col='values', group_col='groups')
# Format: diagonal, non-significant, p<0.001, p<0.01, p<0.05
cmap = ['1', '#fb6a4a',  '#08306b',  '#4292c6', '#c6dbef']
heatmap_args = {'cmap': cmap, 'linewidths': 0.25, 'linecolor': '0.5', 'clip_on': False, 'square': True, 'cbar_ax_bbox': [0.80, 0.35, 0.04, 0.3]}
sp.sign_plot(pc, **heatmap_args)

(<matplotlib.axes._subplots.AxesSubplot at 0x7f67b1636e10>, <matplotlib.colorbar.ColorbarBase at 0x7f67b15efd68>)
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