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Alyssa Salazar
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bidd-aggmap
0
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[9e8054]: / paper / NAR / 02_transcriptome / CNN / 04_visulization.ipynb

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{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from glob import glob\n",
    "import numpy as np\n",
    "from aggmap import AggMap, AggModel"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "flist = glob('./data/*.csv.gzip')\n",
    "flist = pd.Series(flist).sort_values().tolist()\n",
    "fall = []\n",
    "for i in flist:\n",
    "    df1 = pd.read_csv(i, compression='gzip', index_col = 0)\n",
    "    df1['class'] = i.split('/')[-1].split('.csv')[0]\n",
    "    fall.append(df1)\n",
    "    \n",
    "df = pd.concat(fall, axis=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "low_data_class = ['01_ACC', '05_CHOL', '07_DLBC', '08_ESCA', '09_GBM', '11_KICH',\n",
    "       '14_LAML', '19_MESO', '21_PAAD', '22_PCPG', '24_READ', '28_TGCT',\n",
    "       '30_THYM', '32_UCS', '33_UVM']\n",
    "df1 = df[df['class'].isin(low_data_class)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "dfx = df1[df1.columns[:-1]]\n",
    "dfy = df1[df1.columns[-1:]]\n",
    "dfx = np.log2(dfx + 1) #apply log2(x + 1)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2021-01-19 22:21:54,881 - \u001b[32mINFO\u001b[0m - [bidd-aggmap]\u001b[0m - Calculating distance ...\u001b[0m\n",
      "2021-01-19 22:21:55,083 - \u001b[32mINFO\u001b[0m - [bidd-aggmap]\u001b[0m - the number of process is 16\u001b[0m\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|##########| 1583310/1583310 [01:03<00:00, 24935.88it/s]\n",
      "100%|##########| 1583310/1583310 [00:00<00:00, 1826129.78it/s]\n",
      "100%|##########| 1780/1780 [00:03<00:00, 498.68it/s]\n"
     ]
    }
   ],
   "source": [
    "mp = AggMap(dfx.T)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2021-01-19 22:24:45,439 - \u001b[32mINFO\u001b[0m - [bidd-aggmap]\u001b[0m - Applying grid feature map(assignment), this may take several minutes(1~30 min)\u001b[0m\n",
      "2021-01-19 22:24:49,525 - \u001b[32mINFO\u001b[0m - [bidd-aggmap]\u001b[0m - Finished\u001b[0m\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<aggmap.map.AggMap at 0x7f6ee9277ba8>"
      ]
     },
     "execution_count": 28,
     "metadata": {},
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    }
   ],
   "source": [
    "mp.fit(feature_group_list=dfy['class'].tolist(), min_dist = 0.9, verbose = 0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2021-01-19 22:24:49,532 - \u001b[32mINFO\u001b[0m - [bidd-aggmap]\u001b[0m - generate file: ./feature points_1780_correlation_umap_scatter\u001b[0m\n",
      "2021-01-19 22:24:49,577 - \u001b[32mINFO\u001b[0m - [bidd-aggmap]\u001b[0m - save html file to ./feature points_1780_correlation_umap_scatter\u001b[0m\n"
     ]
    },
    {
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