{ "cells": [ { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true }, "outputs": [], "source": [ "import pyupset as pyu\n", "import matplotlib as mpl\n", "import matplotlib.pyplot as plt\n", "from pickle import load\n", "import pandas as pd\n", "import glob \n", "\n", "%matplotlib inline" ] }, { "cell_type": "code", "execution_count": 85, "metadata": {}, "outputs": [], "source": [ "gene_table = pd.read_table('gene_presence_absence.csv', sep=',')" ] }, { "cell_type": "code", "execution_count": 86, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['Gene', 't_centrarchi', 't_lynn', 't_maritimum', 't_mesophilum', 't_ovolyticum', 't_rebecca', 't_soleae', 't_sp47']\n" ] } ], "source": [ "col_names = list(x for x in gene_table.columns if x.startswith('t_'))\n", "col_names.sort()\n", "\n", "col_names.insert(0, 'Gene')\n", "print(col_names)\n", "\n", "gene_table = pd.DataFrame(gene_table, columns=col_names)" ] }, { "cell_type": "code", "execution_count": 87, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | Gene | \n", "t_centrarchi | \n", "t_lynn | \n", "t_maritimum | \n", "t_mesophilum | \n", "t_ovolyticum | \n", "t_rebecca | \n", "t_soleae | \n", "t_sp47 | \n", "
---|---|---|---|---|---|---|---|---|---|
0 | \n", "aadR | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "
1 | \n", "aarA | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "
2 | \n", "aarA_1 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "
3 | \n", "aarA_2 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "
4 | \n", "aat | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "1 | \n", "
5 | \n", "accA | \n", "1 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "
6 | \n", "accA1 | \n", "0 | \n", "1 | \n", "0 | \n", "1 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "
7 | \n", "accA_2 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "
8 | \n", "accB | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
9 | \n", "accC | \n", "1 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "1 | \n", "0 | \n", "