{ "cells": [ { "cell_type": "markdown", "metadata": { "collapsed": false }, "source": [ "# scikit-posthocs\n", "\n", "## Pairwise Multiple Comparisons Post-hoc Tests\n", "\n", "in Python 3 (Ubuntu Linux)\n", "\n", "https://github.com/maximtrp/scikit-posthocs" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "array([[-1. , 0.00119517, 0.00278329],\n", " [ 0.00119517, -1. , 0.18672227],\n", " [ 0.00278329, 0.18672227, -1. ]])" ] }, "execution_count": 1, "metadata": { }, "output_type": "execute_result" } ], "source": [ "import scikit_posthocs as sp\n", "x = [[1,2,3,5,1], [12,31,54], [10,12,6,74,11]]\n", "sp.posthoc_conover(x, p_adjust = 'holm')" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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groupsvalues
0a1
1a2
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" ] }, "execution_count": 2, "metadata": { }, "output_type": "execute_result" } ], "source": [ "import scikit_posthocs as sp\n", "import pandas as pd\n", "x = pd.DataFrame({\"a\": [1,2,3,5,1], \"b\": [12,31,54,62,12], \"c\": [10,12,6,74,11]})\n", "x = x.melt(var_name='groups', value_name='values')\n", "x" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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abc
a-1.0000000.0001090.001853
b0.000109-1.0000000.121659
c0.0018530.121659-1.000000
\n", "
" ] }, "execution_count": 3, "metadata": { }, "output_type": "execute_result" } ], "source": [ "sp.posthoc_conover(x, val_col='values', group_col='groups')" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "(,\n", " )" ] }, "execution_count": 4, "metadata": { }, "output_type": "execute_result" }, { "data": { "image/png": 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}, "execution_count": 4, "metadata": { }, "output_type": "execute_result" } ], "source": [ "pc = sp.posthoc_conover(x, val_col='values', group_col='groups')\n", "heatmap_args = {'linewidths': 0.25, 'linecolor': '0.5', 'clip_on': False, 'square': True, 'cbar_ax_bbox': [0.80, 0.35, 0.04, 0.3]}\n", "sp.sign_plot(pc, **heatmap_args)" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "(,\n", " )" ] }, "execution_count": 5, "metadata": { }, "output_type": "execute_result" }, { "data": { "image/png": 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}, "execution_count": 5, "metadata": { }, "output_type": "execute_result" } ], "source": [ "pc = sp.posthoc_conover(x, val_col='values', group_col='groups')\n", "# Format: diagonal, non-significant, p<0.001, p<0.01, p<0.05\n", "cmap = ['1', '#fb6a4a', '#08306b', '#4292c6', '#c6dbef']\n", "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]}\n", "sp.sign_plot(pc, **heatmap_args)" ] }, { "cell_type": "code", "execution_count": 0, "metadata": { "collapsed": false }, "outputs": [ ], "source": [ ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (Ubuntu Linux)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.5.2" } }, "nbformat": 4, "nbformat_minor": 0 }