Modularity-test1.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import networkx as nx\n",
    "import matplotlib.pyplot as plt\n",
    "from graph import GraphIO\n",
    "\n",
    "import numpy as np \n",
    "from graspologic.utils import symmetrize, to_weighted_edge_list\n",
    "from graspologic.partition import leiden, modularity\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(<networkx.classes.digraph.DiGraph at 0x1c311c0cd48>,\n",
       " {'weight'},\n",
       " {'cell_type0', 'cell_type1', 'dorsoventral', 'hemisphere', 'original_id'},\n",
       " {'Sex', 'Synapse Type', 'Title'})"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GraphIO.load('./worm_wiring/graphs/connectome/Hermaphrodite/0.json')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "ww_H0 = './worm_wiring/graphs/connectome/Hermaphrodite/0.json'\n",
    "ww_H1 = './worm_wiring/graphs/connectome/Hermaphrodite/1.json'\n",
    "ww_H2 = './worm_wiring/graphs/connectome/Hermaphrodite/2.json'\n",
    "ww_M0 = './worm_wiring/graphs/connectome/Male/0.json'\n",
    "ww_M1 = './worm_wiring/graphs/connectome/Male/1.json'\n",
    "ww_M2 = './worm_wiring/graphs/connectome/Male/2.json'\n",
    "ciona = './json_connectomes/ciona.json'\n",
    "ww_c = './json_connectomes/worm_wiring_connectome_0_SL.json'\n",
    "\n",
    "G_wwH0, e_att_wwH0, n_att_wwH0, g_att_wwH0 = GraphIO.load(ww_H0)\n",
    "G_wwH1, e_att_wwH1, n_att_wwH1, g_att_wwH1 = GraphIO.load(ww_H1)\n",
    "G_wwH2, e_att_wwH2, n_att_wwH2, g_att_wwH2 = GraphIO.load(ww_H2)\n",
    "G_wwM0, e_att_wwM0, n_att_wwM0, g_att_wwH0 = GraphIO.load(ww_M0)\n",
    "G_wwM1, e_att_wwM1, n_att_wwM1, g_att_wwH1 = GraphIO.load(ww_M1)\n",
    "G_wwM2, e_att_wwM2, n_att_wwM2, g_att_wwH2 = GraphIO.load(ww_M2)\n",
    "G_ciona, e_att_ciona, n_att_ciona, g_att_ciona = GraphIO.load(ciona)\n",
    "# G_wwc, e_att_wwc, n_att_wwc, g_att_wwc = GraphIO.load(ww_c)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<networkx.classes.graph.Graph at 0x1c312d7fc88>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "G_wwH0 = G_wwH0.to_undirected()\n",
    "G_wwH1 = G_wwH1.to_undirected()\n",
    "G_wwH2 = G_wwH2.to_undirected()\n",
    "G_wwM0 = G_wwM0.to_undirected()\n",
    "G_wwM1 = G_wwM1.to_undirected()\n",
    "G_wwM2 = G_wwM2.to_undirected()\n",
    "# G_wwc = G_wwc.to_undirected()\n",
    "G_wwH0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'coronet3': 100,\n",
       " 'MGIN2R': 50,\n",
       " '124': 115,\n",
       " 'ddNR': 193,\n",
       " 'pns14': 178,\n",
       " 'coronet5': 216,\n",
       " '30': 154,\n",
       " '80': 14,\n",
       " 'pr1': 101,\n",
       " '157': 79,\n",
       " '164': 116,\n",
       " 'pns3': 169,\n",
       " 'murm': 214,\n",
       " '21': 151,\n",
       " '18': 37,\n",
       " '42': 41,\n",
       " '13': 77,\n",
       " '153': 146,\n",
       " 'pr22': 122,\n",
       " 'coronet8': 128,\n",
       " '107': 63,\n",
       " 'pr12': 58,\n",
       " 'ATEN2': 88,\n",
       " 'aaIN2': 53,\n",
       " 'aaIN3': 54,\n",
       " 'ATEN3': 89,\n",
       " 'MN4L': 98,\n",
       " 'pr6': 106,\n",
       " '62': 114,\n",
       " 'BTN2': 91,\n",
       " 'coronet4': 144,\n",
       " 'MN3R': 162,\n",
       " 'pns11': 165,\n",
       " 'AMG5': 87,\n",
       " 'Em2': 92,\n",
       " 'coronet16': 99,\n",
       " 'coronet9': 129,\n",
       " 'Ant1': 68,\n",
       " 'pr14': 172,\n",
       " 'pns6': 179,\n",
       " '46': 182,\n",
       " '24': 5,\n",
       " 'ACIN2L': 194,\n",
       " 'vacIN1': 202,\n",
       " 'pr9': 61,\n",
       " '1': 0,\n",
       " '19': 113,\n",
       " 'pr4': 140,\n",
       " '135': 28,\n",
       " 'pns12': 176,\n",
       " 'pnu': 218,\n",
       " '68': 12,\n",
       " '160': 149,\n",
       " '163': 159,\n",
       " 'ACIN2R': 195,\n",
       " 'PMGN2': 215,\n",
       " '161': 35,\n",
       " '90': 97,\n",
       " '41': 40,\n",
       " 'MN4R': 204,\n",
       " 'MN5R': 209,\n",
       " 'pna': 199,\n",
       " '123': 1,\n",
       " '126': 25,\n",
       " '147': 31,\n",
       " '121': 24,\n",
       " '100': 18,\n",
       " 'MN3L': 51,\n",
       " '3': 38,\n",
       " '116': 73,\n",
       " '94': 85,\n",
       " 'pr2': 94,\n",
       " 'AMG2': 86,\n",
       " 'BTN3': 120,\n",
       " 'coronet1': 55,\n",
       " 'pr5': 60,\n",
       " '85': 160,\n",
       " '57': 188,\n",
       " '55': 9,\n",
       " 'pnx': 220,\n",
       " 'bm-noto': 210,\n",
       " 'coronet7': 183,\n",
       " 'mur': 213,\n",
       " 'NeckNR': 156,\n",
       " '130': 26,\n",
       " 'midtail1': 206,\n",
       " '127': 76,\n",
       " '92': 117,\n",
       " '86': 44,\n",
       " 'lens6': 134,\n",
       " 'ddNL': 139,\n",
       " 'MGIN3R': 157,\n",
       " 'pnb': 200,\n",
       " '20': 153,\n",
       " 'midtail7': 221,\n",
       " 'ukn2': 17,\n",
       " '113': 65,\n",
       " 'coronet10': 56,\n",
       " 'pns13': 180,\n",
       " 'pnh': 217,\n",
       " '142': 30,\n",
       " 'mul': 211,\n",
       " '152': 33,\n",
       " 'pns1': 133,\n",
       " 'trIN': 15,\n",
       " 'pre': 132,\n",
       " '4': 7,\n",
       " '105': 19,\n",
       " 'MGIN3L': 142,\n",
       " '181': 161,\n",
       " 'AMG7': 135,\n",
       " '74': 83,\n",
       " '6': 168,\n",
       " '70': 13,\n",
       " '25': 173,\n",
       " 'pns4': 170,\n",
       " '120': 23,\n",
       " 'pr18': 121,\n",
       " '159': 111,\n",
       " '134': 27,\n",
       " 'prf': 110,\n",
       " '2': 2,\n",
       " 'lens7': 69,\n",
       " 'pr13': 131,\n",
       " 'BTN4': 136,\n",
       " '15': 32,\n",
       " '88': 155,\n",
       " '140': 29,\n",
       " 'MN2R': 158,\n",
       " 'AMG3': 164,\n",
       " '43': 166,\n",
       " 'ukn': 16,\n",
       " '119': 22,\n",
       " 'prb': 123,\n",
       " 'coronet12': 147,\n",
       " 'bm': 125,\n",
       " '35': 175,\n",
       " 'ATEN1': 177,\n",
       " '78': 43,\n",
       " 'AMG1': 150,\n",
       " '112': 21,\n",
       " 'pr15': 70,\n",
       " 'MN2L': 143,\n",
       " '103': 71,\n",
       " '73': 42,\n",
       " 'ATEN4': 174,\n",
       " 'pns9': 181,\n",
       " '143': 67,\n",
       " '114': 66,\n",
       " 'midtail4': 207,\n",
       " 'coronet6': 145,\n",
       " '122': 74,\n",
       " 'AMG6': 119,\n",
       " '5': 187,\n",
       " '108': 72,\n",
       " '38': 39,\n",
       " 'pnc': 198,\n",
       " 'MN1L': 137,\n",
       " '59': 10,\n",
       " 'ACIN1L': 192,\n",
       " 'pr21': 59,\n",
       " '40': 185,\n",
       " 'pr20': 95,\n",
       " 'pr16': 102,\n",
       " 'pr23': 104,\n",
       " '33': 6,\n",
       " 'Em1': 47,\n",
       " 'pra': 109,\n",
       " 'pns7': 171,\n",
       " 'pns5': 190,\n",
       " 'prg': 201,\n",
       " '61': 82,\n",
       " 'pr11': 57,\n",
       " '65': 11,\n",
       " 'pr7': 107,\n",
       " 'MGIN1R': 112,\n",
       " 'AMG4': 118,\n",
       " 'pr10': 130,\n",
       " 'PMGN1': 205,\n",
       " 'mulm': 212,\n",
       " 'aaIN1': 52,\n",
       " '60': 126,\n",
       " 'coronet11': 127,\n",
       " 'pr19': 103,\n",
       " 'midtail2': 208,\n",
       " '162': 80,\n",
       " '96': 45,\n",
       " '16': 34,\n",
       " '79': 141,\n",
       " 'pns10': 184,\n",
       " '48': 8,\n",
       " '101': 62,\n",
       " '23': 4,\n",
       " '106': 20,\n",
       " '131': 78,\n",
       " '125': 75,\n",
       " 'pr3': 105,\n",
       " 'Ant2': 46,\n",
       " 'MGIN1L': 48,\n",
       " '29': 81,\n",
       " 'pr8': 108,\n",
       " 'prc': 124,\n",
       " 'MN1R': 138,\n",
       " 'pns2': 189,\n",
       " 'pnf': 197,\n",
       " '110': 64,\n",
       " 'coronet14': 163,\n",
       " 'MN5L': 203,\n",
       " 'coronet2': 191,\n",
       " '22': 3,\n",
       " '17': 36,\n",
       " 'prd': 148,\n",
       " 'BTN1': 90,\n",
       " '50': 152,\n",
       " 'NeckNL': 196,\n",
       " '177': 167,\n",
       " 'pnw': 219,\n",
       " '93': 84,\n",
       " '138': 96,\n",
       " 'MGIN2L': 49,\n",
       " '44': 186,\n",
       " 'pr17': 93}"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "leiden_wwH0 = leiden(G_wwH0)\n",
    "leiden_wwH1 = leiden(G_wwH1)\n",
    "leiden_wwH2 = leiden(G_wwH2)\n",
    "leiden_wwM0 = leiden(G_wwM0)\n",
    "leiden_wwM1 = leiden(G_wwM1)\n",
    "leiden_wwM2 = leiden(G_wwM2)\n",
    "leiden_ciona = leiden(G_ciona)\n",
    "# leiden_wwc = leiden(G_wwc)\n",
    "leiden_ciona"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "m_wwH0 = modularity(G_wwH0,leiden_wwH0)\n",
    "m_wwH1 = modularity(G_wwH1,leiden_wwH1)\n",
    "m_wwH2 = modularity(G_wwH2,leiden_wwH2)\n",
    "m_wwM0 = modularity(G_wwM0,leiden_wwM0)\n",
    "m_wwM1 = modularity(G_wwM1,leiden_wwM1)\n",
    "m_wwM2 = modularity(G_wwM2,leiden_wwM2)\n",
    "m_ciona = modularity(G_ciona,leiden_ciona)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.5421591264290776 0.6606203599995307 0.6649342629949332 0.5648920607094574 0.7568173525578548 0.6649342629949332\n",
      "nan\n"
     ]
    }
   ],
   "source": [
    "print(m_wwH0, m_wwH1, m_wwH2, m_wwM0, m_wwM1, m_wwH2)\n",
    "print(m_ciona)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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