{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# This tutorial provides examples of codes for static Manhattan and QQ plots. \n", "\n" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "# In order to view the figures in this notebook it is necessary to included the following line\n", "%matplotlib inline" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "# import pandas and qmplot functions\n", "import pandas as pd\n", "import matplotlib.pyplot as plt\n", "from qmplot import manhattanplot, qqplot" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | #CHROM | \n", "POS | \n", "ID | \n", "REF | \n", "ALT | \n", "A1 | \n", "TEST | \n", "OBS_CT | \n", "BETA | \n", "SE | \n", "T_STAT | \n", "P | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "chr1 | \n", "904165 | \n", "1_904165 | \n", "G | \n", "A | \n", "A | \n", "ADD | \n", "282 | \n", "-0.090890 | \n", "0.195476 | \n", "-0.464967 | \n", "0.642344 | \n", "
1 | \n", "chr1 | \n", "1563691 | \n", "1_1563691 | \n", "T | \n", "G | \n", "G | \n", "ADD | \n", "271 | \n", "0.447021 | \n", "0.422194 | \n", "1.058800 | \n", "0.290715 | \n", "
2 | \n", "chr1 | \n", "1707740 | \n", "1_1707740 | \n", "T | \n", "G | \n", "G | \n", "ADD | \n", "283 | \n", "0.149911 | \n", "0.161387 | \n", "0.928888 | \n", "0.353805 | \n", "
3 | \n", "chr1 | \n", "2284195 | \n", "1_2284195 | \n", "T | \n", "C | \n", "C | \n", "ADD | \n", "275 | \n", "-0.024704 | \n", "0.139660 | \n", "-0.176887 | \n", "0.859739 | \n", "
4 | \n", "chr1 | \n", "2779043 | \n", "1_2779043 | \n", "T | \n", "C | \n", "T | \n", "ADD | \n", "272 | \n", "-0.111771 | \n", "0.139929 | \n", "-0.798770 | \n", "0.425182 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
9219 | \n", "chrX | \n", "151616708 | \n", "X_151616708 | \n", "A | \n", "G | \n", "A | \n", "ADD | \n", "265 | \n", "-0.102974 | \n", "0.107027 | \n", "-0.962127 | \n", "0.336946 | \n", "
9220 | \n", "chrX | \n", "152091153 | \n", "X_152091153 | \n", "A | \n", "C | \n", "A | \n", "ADD | \n", "273 | \n", "-0.298747 | \n", "0.142878 | \n", "-2.090920 | \n", "0.037545 | \n", "
9221 | \n", "chrX | \n", "152596189 | \n", "X_152596189 | \n", "G | \n", "A | \n", "G | \n", "ADD | \n", "275 | \n", "-0.057860 | \n", "0.126889 | \n", "-0.455988 | \n", "0.648792 | \n", "
9222 | \n", "chrX | \n", "152660491 | \n", "X_152660491 | \n", "C | \n", "G | \n", "G | \n", "ADD | \n", "266 | \n", "0.050713 | \n", "0.122452 | \n", "0.414148 | \n", "0.679131 | \n", "
9223 | \n", "chrX | \n", "154087368 | \n", "X_154087368 | \n", "T | \n", "A | \n", "T | \n", "ADD | \n", "277 | \n", "-0.123774 | \n", "0.173297 | \n", "-0.714234 | \n", "0.475739 | \n", "
9217 rows × 12 columns
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