1_preprocess_adata.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import scanpy as sc\n",
    "import os\n",
    "import re\n",
    "import scipy as scp\n",
    "import pandas as pd\n",
    "import scvelo as scv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[AnnData object with n_obs × n_vars = 138540 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116408 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116486 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 159643 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144376 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 106378 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 134343 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 111044 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 153254 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116974 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 145744 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 141065 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135125 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 134412 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151317 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 101393 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 129784 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 188624 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144137 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 209885 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 111928 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144621 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 114267 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 132227 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 109797 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 107397 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 156809 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 157825 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 118347 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 152265 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 108733 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143497 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 109151 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 118370 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143505 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 118165 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 114938 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143684 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 161416 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 191856 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 147851 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151286 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 103316 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 133224 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 155543 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 141467 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 111805 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144706 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 156220 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 145707 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 192529 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 106611 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 103860 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 140575 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 152396 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 158622 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135299 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 105084 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 157231 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 147738 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 191622 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 138178 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151624 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151948 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151073 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 140444 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 154064 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 132910 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 154833 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 193651 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144124 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116748 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 105130 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 134420 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 132825 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 158323 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 138483 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135058 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 159465 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 154041 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 104209 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151079 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 109226 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135753 × 60623 \n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143997 × 60623 \n",
       "     layers: 'spliced', 'unspliced']"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Read the downloaded output files from the folders\n",
    "adataNames = os.listdir('./adataObjs/')\n",
    "adataList = []\n",
    "for aN in adataNames:\n",
    "    adataList.append(sc.read_h5ad('./adataObjs/'+aN))\n",
    "adataList"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "samples = []\n",
    "for an in adataNames:\n",
    "    samples.append(re.search('S.*[0-9]_',an).group()[:-1])\n",
    "#for z in zip(adataNames,samples):\n",
    "    #print(z)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[AnnData object with n_obs × n_vars = 138540 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116408 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116486 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 159643 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144376 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 106378 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 134343 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 111044 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 153254 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116974 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 145744 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 141065 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135125 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 134412 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151317 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 101393 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 129784 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 188624 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144137 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 209885 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 111928 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144621 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 114267 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 132227 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 109797 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 107397 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 156809 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 157825 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 118347 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 152265 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 108733 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143497 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 109151 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 118370 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143505 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 118165 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 114938 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143684 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 161416 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 191856 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 147851 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151286 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 103316 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 133224 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 155543 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 141467 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 111805 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144706 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 156220 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 145707 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 192529 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 106611 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 103860 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 140575 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 152396 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 158622 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135299 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 105084 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 157231 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 147738 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 191622 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 138178 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151624 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151948 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151073 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 140444 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 154064 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 132910 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 154833 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 193651 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 144124 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 116748 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 105130 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 134420 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 132825 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 158323 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 138483 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135058 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 159465 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 154041 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 104209 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 151079 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 109226 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 135753 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 143997 × 60623 \n",
       "     obs: 'folder'\n",
       "     layers: 'spliced', 'unspliced']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "for i,adata in enumerate(adataList):\n",
    "    adata.obs[\"folder\"] = samples[i]\n",
    "adataList"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# check if the barcodes are unique\n",
    "uniqueCheck = []\n",
    "for adata in adataList:\n",
    "    uniqueCheck.append(len(set(adata.obs.index)) == len(adata.obs.index))\n",
    "all(uniqueCheck)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "layers concatenation is not yet available for 'outer' intersection and will be ignored.\n"
     ]
    },
    {
     "ename": "MemoryError",
     "evalue": "Unable to allocate array with shape (191856, 60623) and data type float32",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mMemoryError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-b1e3916c6298>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0madata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0madataList\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconcatenate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0madataList\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'outer'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0madata\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/conda/envs/Fertig_Python_3_7/lib/python3.7/site-packages/anndata/core/anndata.py\u001b[0m in \u001b[0;36mconcatenate\u001b[0;34m(self, join, batch_key, batch_categories, index_unique, *adatas)\u001b[0m\n\u001b[1;32m   1861\u001b[0m                 \u001b[0;31m# constructed like that\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1862\u001b[0m                 X[obs_i:obs_i+ad.n_obs,\n\u001b[0;32m-> 1863\u001b[0;31m                   var_names.isin(vars_intersect)] = ad[:, vars_intersect].X\n\u001b[0m\u001b[1;32m   1864\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1865\u001b[0m                 \u001b[0mXs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mad\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvars_intersect\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mX\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/conda/envs/Fertig_Python_3_7/lib/python3.7/site-packages/scipy/sparse/lil.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, x)\u001b[0m\n\u001b[1;32m    344\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_set_intXint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    345\u001b[0m         \u001b[0;31m# Everything else takes the normal path.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 346\u001b[0;31m         \u001b[0mIndexMixin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__setitem__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    348\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_mul_scalar\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mother\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/conda/envs/Fertig_Python_3_7/lib/python3.7/site-packages/scipy/sparse/_index.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, x)\u001b[0m\n\u001b[1;32m    116\u001b[0m             \u001b[0mx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtocoo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    117\u001b[0m             \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msum_duplicates\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 118\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_set_arrayXarray_sparse\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    119\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    120\u001b[0m             \u001b[0;31m# Make x and i into the same shape\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/conda/envs/Fertig_Python_3_7/lib/python3.7/site-packages/scipy/sparse/lil.py\u001b[0m in \u001b[0;36m_set_arrayXarray_sparse\u001b[0;34m(self, row, col, x)\u001b[0m\n\u001b[1;32m    330\u001b[0m             \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    331\u001b[0m         \u001b[0;31m# Fall back to densifying x\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 332\u001b[0;31m         \u001b[0mx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0masarray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtoarray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    333\u001b[0m         \u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_broadcast_arrays\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrow\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    334\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_set_arrayXarray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrow\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcol\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/conda/envs/Fertig_Python_3_7/lib/python3.7/site-packages/scipy/sparse/coo.py\u001b[0m in \u001b[0;36mtoarray\u001b[0;34m(self, order, out)\u001b[0m\n\u001b[1;32m    321\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mtoarray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0morder\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    322\u001b[0m         \u001b[0;34m\"\"\"See the docstring for `spmatrix.toarray`.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 323\u001b[0;31m         \u001b[0mB\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_process_toarray_args\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0morder\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    324\u001b[0m         \u001b[0mfortran\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mB\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mflags\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_contiguous\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    325\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mfortran\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mB\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mflags\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mc_contiguous\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/conda/envs/Fertig_Python_3_7/lib/python3.7/site-packages/scipy/sparse/base.py\u001b[0m in \u001b[0;36m_process_toarray_args\u001b[0;34m(self, order, out)\u001b[0m\n\u001b[1;32m   1184\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mout\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1185\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1186\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mzeros\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0morder\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0morder\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1187\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1188\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mMemoryError\u001b[0m: Unable to allocate array with shape (191856, 60623) and data type float32"
     ]
    }
   ],
   "source": [
    "adata = adataList[0].concatenate(adataList[1:],join='outer')\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[AnnData object with n_obs × n_vars = 3320 × 15465 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1834 × 13797 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2167 × 14809 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1904 × 15976 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 4270 × 16736 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1348 × 14027 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1396 × 15259 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2607 × 14042 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2570 × 16806 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2704 × 14853 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2748 × 15574 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 4256 × 16751 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1828 × 14022 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1395 × 15270 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2580 × 16795 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3329 × 14640 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3838 × 16267 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1943 × 15228 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 4264 × 16866 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 5314 × 16673 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2624 × 14062 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2745 × 15417 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2421 × 15245 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1833 × 13885 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2163 × 14121 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3390 × 15093 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1909 × 15908 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3442 × 15221 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2700 × 14993 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2233 × 16474 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2168 × 14018 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2276 × 15463 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3339 × 15139 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1824 × 14555 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2279 × 15448 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1823 × 13913 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2172 × 14808 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 4246 × 16823 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3127 × 15225 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1955 × 15188 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2237 × 16298 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2241 × 16329 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3293 × 14782 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3847 × 16286 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2778 × 16562 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2749 × 15309 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2424 × 15146 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2276 × 15539 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2779 × 16675 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 4244 × 16918 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1956 × 15324 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3024 × 14199 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3042 × 14068 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3329 × 15649 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2575 × 16702 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3239 × 15222 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1397 × 15330 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1349 × 13928 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1924 × 15831 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2572 × 16711 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1948 × 15217 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3325 × 15457 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2587 × 16650 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2235 × 16326 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2778 × 16548 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2280 × 15361 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1910 × 15811 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3848 × 16312 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2782 × 16518 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1949 × 15386 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2761 × 15436 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1826 × 14418 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1356 × 13952 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3843 × 16448 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3864 × 16267 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1915 × 15860 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3331 × 15428 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1398 × 15212 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3094 × 15336 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3021 × 15250 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 1348 × 13873 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2238 × 16390 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2614 × 13937 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 3324 × 15467 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced',\n",
       " AnnData object with n_obs × n_vars = 2279 × 15380 \n",
       "     obs: 'folder', 'n_genes'\n",
       "     var: 'n_cells'\n",
       "     layers: 'spliced', 'unspliced']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#filter cells and genes\n",
    "# now I realised that this step is wrong because it doesn't contain all data from a cell in one row\n",
    "for adata in adataList:\n",
    "    sc.pp.filter_cells(adata,min_genes=200)\n",
    "    sc.pp.filter_genes(adata,min_cells=3)\n",
    "adataList"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "layers concatenation is not yet available for 'outer' intersection and will be ignored.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 223413 × 22555 \n",
       "    obs: 'batch', 'folder', 'n_genes'\n",
       "    var: 'n_cells-0', 'n_cells-1', 'n_cells-2', 'n_cells-3', 'n_cells-4', 'n_cells-5', 'n_cells-6', 'n_cells-7', 'n_cells-8', 'n_cells-9', 'n_cells-10', 'n_cells-11', 'n_cells-12', 'n_cells-13', 'n_cells-14', 'n_cells-15', 'n_cells-16', 'n_cells-17', 'n_cells-18', 'n_cells-19', 'n_cells-20', 'n_cells-21', 'n_cells-22', 'n_cells-23', 'n_cells-24', 'n_cells-25', 'n_cells-26', 'n_cells-27', 'n_cells-28', 'n_cells-29', 'n_cells-30', 'n_cells-31', 'n_cells-32', 'n_cells-33', 'n_cells-34', 'n_cells-35', 'n_cells-36', 'n_cells-37', 'n_cells-38', 'n_cells-39', 'n_cells-40', 'n_cells-41', 'n_cells-42', 'n_cells-43', 'n_cells-44', 'n_cells-45', 'n_cells-46', 'n_cells-47', 'n_cells-48', 'n_cells-49', 'n_cells-50', 'n_cells-51', 'n_cells-52', 'n_cells-53', 'n_cells-54', 'n_cells-55', 'n_cells-56', 'n_cells-57', 'n_cells-58', 'n_cells-59', 'n_cells-60', 'n_cells-61', 'n_cells-62', 'n_cells-63', 'n_cells-64', 'n_cells-65', 'n_cells-66', 'n_cells-67', 'n_cells-68', 'n_cells-69', 'n_cells-70', 'n_cells-71', 'n_cells-72', 'n_cells-73', 'n_cells-74', 'n_cells-75', 'n_cells-76', 'n_cells-77', 'n_cells-78', 'n_cells-79', 'n_cells-80', 'n_cells-81', 'n_cells-82', 'n_cells-83', 'n_cells-84'"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata = adataList[0].concatenate(adataList[1:],join='outer')\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "obs = []\n",
    "for barcode in adata.obs.index:\n",
    "    obs.append(barcode)\n",
    "len(obs) == len(set(obs))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "#store spliced and unspliced for concatenation separately because it will get concat\n",
    "s = []\n",
    "u = []\n",
    "for ad in adataList:\n",
    "    s.append(scp.sparse.csr_matrix(ad.layers['spliced']))\n",
    "    u.append(scp.sparse.csr_matrix(ad.layers['unspliced']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Convert the spliced and unspliced matrices to pandas dataframe\n",
    "pdS = []\n",
    "pdU = []\n",
    "for i,sm in enumerate(s):\n",
    "    pdS.append(pd.DataFrame(sm.toarray(),index=adataList[i].obs.index,columns=adataList[i].var.index))\n",
    "for i,um in enumerate(u): \n",
    "    pdU.append(pd.DataFrame(um.toarray(),index=adataList[i].obs.index,columns=adataList[i].var.index))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "#concatenate the data\n",
    "pdSCon = pd.concat(pdS,sort=False)\n",
    "pdUCon = pd.concat(pdU,sort=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Rearrange the gene names (cols) to match with the adata concatenation\n",
    "pdSCon = pdSCon.loc[:,adata.var.index]\n",
    "pdUCon = pdUCon.loc[:,adata.var.index]\n",
    "#fill na with 0\n",
    "pdSCon.fillna(0,inplace=True)\n",
    "pdUCon.fillna(0,inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "equal = 0\n",
    "for i,val in enumerate(pdSCon.columns):\n",
    "    if val == adata.var.index[i]:\n",
    "        equal +=1\n",
    "equal == len(pdSCon.columns)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.layers['spliced'] = scp.sparse.csr_matrix(pdSCon.values)\n",
    "adata.layers['unspliced'] = scp.sparse.csr_matrix(pdUCon.values)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Abundance of ['spliced', 'unspliced']: [0.77 0.23]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 223413 × 22555 \n",
       "    obs: 'batch', 'folder', 'n_genes'\n",
       "    var: 'n_cells-0', 'n_cells-1', 'n_cells-2', 'n_cells-3', 'n_cells-4', 'n_cells-5', 'n_cells-6', 'n_cells-7', 'n_cells-8', 'n_cells-9', 'n_cells-10', 'n_cells-11', 'n_cells-12', 'n_cells-13', 'n_cells-14', 'n_cells-15', 'n_cells-16', 'n_cells-17', 'n_cells-18', 'n_cells-19', 'n_cells-20', 'n_cells-21', 'n_cells-22', 'n_cells-23', 'n_cells-24', 'n_cells-25', 'n_cells-26', 'n_cells-27', 'n_cells-28', 'n_cells-29', 'n_cells-30', 'n_cells-31', 'n_cells-32', 'n_cells-33', 'n_cells-34', 'n_cells-35', 'n_cells-36', 'n_cells-37', 'n_cells-38', 'n_cells-39', 'n_cells-40', 'n_cells-41', 'n_cells-42', 'n_cells-43', 'n_cells-44', 'n_cells-45', 'n_cells-46', 'n_cells-47', 'n_cells-48', 'n_cells-49', 'n_cells-50', 'n_cells-51', 'n_cells-52', 'n_cells-53', 'n_cells-54', 'n_cells-55', 'n_cells-56', 'n_cells-57', 'n_cells-58', 'n_cells-59', 'n_cells-60', 'n_cells-61', 'n_cells-62', 'n_cells-63', 'n_cells-64', 'n_cells-65', 'n_cells-66', 'n_cells-67', 'n_cells-68', 'n_cells-69', 'n_cells-70', 'n_cells-71', 'n_cells-72', 'n_cells-73', 'n_cells-74', 'n_cells-75', 'n_cells-76', 'n_cells-77', 'n_cells-78', 'n_cells-79', 'n_cells-80', 'n_cells-81', 'n_cells-82', 'n_cells-83', 'n_cells-84'\n",
       "    layers: 'spliced', 'unspliced'"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "scv.utils.show_proportions(adata)\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>batch</th>\n",
       "      <th>folder</th>\n",
       "      <th>n_genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCGATTCT-0</th>\n",
       "      <td>0</td>\n",
       "      <td>S4_L007</td>\n",
       "      <td>2596</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCTTTGGT-0</th>\n",
       "      <td>0</td>\n",
       "      <td>S4_L007</td>\n",
       "      <td>329</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGGCCCTCA-0</th>\n",
       "      <td>0</td>\n",
       "      <td>S4_L007</td>\n",
       "      <td>2178</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGTAGCCGA-0</th>\n",
       "      <td>0</td>\n",
       "      <td>S4_L007</td>\n",
       "      <td>253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTAGCGCTC-0</th>\n",
       "      <td>0</td>\n",
       "      <td>S4_L007</td>\n",
       "      <td>420</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   batch   folder  n_genes\n",
       "AAACCTGAGCGATTCT-0     0  S4_L007     2596\n",
       "AAACCTGAGCTTTGGT-0     0  S4_L007      329\n",
       "AAACCTGAGGCCCTCA-0     0  S4_L007     2178\n",
       "AAACCTGAGTAGCCGA-0     0  S4_L007      253\n",
       "AAACCTGGTAGCGCTC-0     0  S4_L007      420"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.obs.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n_cells-0</th>\n",
       "      <th>n_cells-1</th>\n",
       "      <th>n_cells-2</th>\n",
       "      <th>n_cells-3</th>\n",
       "      <th>n_cells-4</th>\n",
       "      <th>n_cells-5</th>\n",
       "      <th>n_cells-6</th>\n",
       "      <th>n_cells-7</th>\n",
       "      <th>n_cells-8</th>\n",
       "      <th>n_cells-9</th>\n",
       "      <th>...</th>\n",
       "      <th>n_cells-75</th>\n",
       "      <th>n_cells-76</th>\n",
       "      <th>n_cells-77</th>\n",
       "      <th>n_cells-78</th>\n",
       "      <th>n_cells-79</th>\n",
       "      <th>n_cells-80</th>\n",
       "      <th>n_cells-81</th>\n",
       "      <th>n_cells-82</th>\n",
       "      <th>n_cells-83</th>\n",
       "      <th>n_cells-84</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000001460.18</th>\n",
       "      <td>89.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>105.0</td>\n",
       "      <td>177.0</td>\n",
       "      <td>41.0</td>\n",
       "      <td>58.0</td>\n",
       "      <td>50.0</td>\n",
       "      <td>179.0</td>\n",
       "      <td>78.0</td>\n",
       "      <td>...</td>\n",
       "      <td>112.0</td>\n",
       "      <td>101.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>62.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>108.0</td>\n",
       "      <td>49.0</td>\n",
       "      <td>88.0</td>\n",
       "      <td>68.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000001461.17</th>\n",
       "      <td>405.0</td>\n",
       "      <td>181.0</td>\n",
       "      <td>231.0</td>\n",
       "      <td>369.0</td>\n",
       "      <td>635.0</td>\n",
       "      <td>229.0</td>\n",
       "      <td>382.0</td>\n",
       "      <td>212.0</td>\n",
       "      <td>645.0</td>\n",
       "      <td>264.0</td>\n",
       "      <td>...</td>\n",
       "      <td>399.0</td>\n",
       "      <td>427.0</td>\n",
       "      <td>400.0</td>\n",
       "      <td>368.0</td>\n",
       "      <td>359.0</td>\n",
       "      <td>241.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>190.0</td>\n",
       "      <td>403.0</td>\n",
       "      <td>413.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000010072.16</th>\n",
       "      <td>244.0</td>\n",
       "      <td>198.0</td>\n",
       "      <td>142.0</td>\n",
       "      <td>290.0</td>\n",
       "      <td>331.0</td>\n",
       "      <td>210.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>148.0</td>\n",
       "      <td>359.0</td>\n",
       "      <td>144.0</td>\n",
       "      <td>...</td>\n",
       "      <td>296.0</td>\n",
       "      <td>241.0</td>\n",
       "      <td>319.0</td>\n",
       "      <td>353.0</td>\n",
       "      <td>352.0</td>\n",
       "      <td>178.0</td>\n",
       "      <td>288.0</td>\n",
       "      <td>149.0</td>\n",
       "      <td>195.0</td>\n",
       "      <td>366.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000009780.15</th>\n",
       "      <td>123.0</td>\n",
       "      <td>124.0</td>\n",
       "      <td>131.0</td>\n",
       "      <td>119.0</td>\n",
       "      <td>343.0</td>\n",
       "      <td>135.0</td>\n",
       "      <td>233.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>301.0</td>\n",
       "      <td>114.0</td>\n",
       "      <td>...</td>\n",
       "      <td>116.0</td>\n",
       "      <td>97.0</td>\n",
       "      <td>251.0</td>\n",
       "      <td>204.0</td>\n",
       "      <td>228.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>235.0</td>\n",
       "      <td>63.0</td>\n",
       "      <td>99.0</td>\n",
       "      <td>254.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000048707.15</th>\n",
       "      <td>218.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>88.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>196.0</td>\n",
       "      <td>80.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>187.0</td>\n",
       "      <td>80.0</td>\n",
       "      <td>...</td>\n",
       "      <td>130.0</td>\n",
       "      <td>224.0</td>\n",
       "      <td>123.0</td>\n",
       "      <td>94.0</td>\n",
       "      <td>105.0</td>\n",
       "      <td>63.0</td>\n",
       "      <td>164.0</td>\n",
       "      <td>82.0</td>\n",
       "      <td>208.0</td>\n",
       "      <td>121.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 85 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    n_cells-0  n_cells-1  n_cells-2  n_cells-3  n_cells-4  \\\n",
       "ENSG00000001460.18       89.0       32.0       55.0      105.0      177.0   \n",
       "ENSG00000001461.17      405.0      181.0      231.0      369.0      635.0   \n",
       "ENSG00000010072.16      244.0      198.0      142.0      290.0      331.0   \n",
       "ENSG00000009780.15      123.0      124.0      131.0      119.0      343.0   \n",
       "ENSG00000048707.15      218.0       61.0       88.0      126.0      196.0   \n",
       "\n",
       "                    n_cells-5  n_cells-6  n_cells-7  n_cells-8  n_cells-9  \\\n",
       "ENSG00000001460.18       41.0       58.0       50.0      179.0       78.0   \n",
       "ENSG00000001461.17      229.0      382.0      212.0      645.0      264.0   \n",
       "ENSG00000010072.16      210.0      330.0      148.0      359.0      144.0   \n",
       "ENSG00000009780.15      135.0      233.0       55.0      301.0      114.0   \n",
       "ENSG00000048707.15       80.0      126.0       74.0      187.0       80.0   \n",
       "\n",
       "                       ...      n_cells-75  n_cells-76  n_cells-77  \\\n",
       "ENSG00000001460.18     ...           112.0       101.0        56.0   \n",
       "ENSG00000001461.17     ...           399.0       427.0       400.0   \n",
       "ENSG00000010072.16     ...           296.0       241.0       319.0   \n",
       "ENSG00000009780.15     ...           116.0        97.0       251.0   \n",
       "ENSG00000048707.15     ...           130.0       224.0       123.0   \n",
       "\n",
       "                    n_cells-78  n_cells-79  n_cells-80  n_cells-81  \\\n",
       "ENSG00000001460.18        61.0        62.0        36.0       108.0   \n",
       "ENSG00000001461.17       368.0       359.0       241.0       438.0   \n",
       "ENSG00000010072.16       353.0       352.0       178.0       288.0   \n",
       "ENSG00000009780.15       204.0       228.0       151.0       235.0   \n",
       "ENSG00000048707.15        94.0       105.0        63.0       164.0   \n",
       "\n",
       "                    n_cells-82  n_cells-83  n_cells-84  \n",
       "ENSG00000001460.18        49.0        88.0        68.0  \n",
       "ENSG00000001461.17       190.0       403.0       413.0  \n",
       "ENSG00000010072.16       149.0       195.0       366.0  \n",
       "ENSG00000009780.15        63.0        99.0       254.0  \n",
       "ENSG00000048707.15        82.0       208.0       121.0  \n",
       "\n",
       "[5 rows x 85 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.var.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>folder</th>\n",
       "      <th>n_genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCGATTCT-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>2596</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCTTTGGT-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>329</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGGCCCTCA-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>2178</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGTAGCCGA-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTAGCGCTC-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>420</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                     folder  n_genes\n",
       "AAACCTGAGCGATTCT-0  S4_L007     2596\n",
       "AAACCTGAGCTTTGGT-0  S4_L007      329\n",
       "AAACCTGAGGCCCTCA-0  S4_L007     2178\n",
       "AAACCTGAGTAGCCGA-0  S4_L007      253\n",
       "AAACCTGGTAGCGCTC-0  S4_L007      420"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.obs.drop('batch',axis=1,inplace=True)\n",
    "adata.obs.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "#convert na to 0\n",
    "adata.var.fillna(0,inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n_cells</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000001460.18</th>\n",
       "      <td>7252.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000001461.17</th>\n",
       "      <td>31838.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000010072.16</th>\n",
       "      <td>22712.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000009780.15</th>\n",
       "      <td>15246.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000048707.15</th>\n",
       "      <td>11175.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000059588.10</th>\n",
       "      <td>14109.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000041988.15</th>\n",
       "      <td>17368.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000049245.13</th>\n",
       "      <td>73043.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000052723.11</th>\n",
       "      <td>60322.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000058799.15</th>\n",
       "      <td>22188.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000060642.10</th>\n",
       "      <td>18859.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000069424.15</th>\n",
       "      <td>9673.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000074964.17</th>\n",
       "      <td>5560.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000081870.11</th>\n",
       "      <td>87432.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000083444.17</th>\n",
       "      <td>39605.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000076321.11</th>\n",
       "      <td>13877.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000069702.11</th>\n",
       "      <td>1063.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000074800.16</th>\n",
       "      <td>180479.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000097046.13</th>\n",
       "      <td>12540.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000097096.9</th>\n",
       "      <td>7037.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000031698.13</th>\n",
       "      <td>104264.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116128.11</th>\n",
       "      <td>4346.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116205.14</th>\n",
       "      <td>6010.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116209.12</th>\n",
       "      <td>124887.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116251.11</th>\n",
       "      <td>60890.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116455.14</th>\n",
       "      <td>16696.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116667.14</th>\n",
       "      <td>2166.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116670.15</th>\n",
       "      <td>70475.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116688.16</th>\n",
       "      <td>24551.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000116691.11</th>\n",
       "      <td>30275.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000134516.17</th>\n",
       "      <td>392.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000255245.4</th>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000241993.1</th>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000241135.6</th>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000158882.15</th>\n",
       "      <td>151.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000234884.2</th>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000234076.1</th>\n",
       "      <td>257.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000261678.3</th>\n",
       "      <td>175.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000179958.9</th>\n",
       "      <td>165.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000227080.2</th>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000254418.1</th>\n",
       "      <td>460.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000102575.13</th>\n",
       "      <td>126.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000271553.1</th>\n",
       "      <td>556.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000223298.1</th>\n",
       "      <td>263.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000231346.5</th>\n",
       "      <td>142.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000143839.15</th>\n",
       "      <td>75.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000174450.12</th>\n",
       "      <td>55.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000244694.7</th>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000262343.1</th>\n",
       "      <td>13.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000239323.1</th>\n",
       "      <td>33.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000161835.11</th>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000173809.18</th>\n",
       "      <td>124.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000237126.8</th>\n",
       "      <td>62.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000236699.9</th>\n",
       "      <td>12.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000242252.2</th>\n",
       "      <td>149.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000242461.1</th>\n",
       "      <td>35.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000231364.3</th>\n",
       "      <td>23.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000288023.1</th>\n",
       "      <td>309.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000211445.12</th>\n",
       "      <td>34066.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000267547.1</th>\n",
       "      <td>631.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>22555 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                     n_cells\n",
       "ENSG00000001460.18    7252.0\n",
       "ENSG00000001461.17   31838.0\n",
       "ENSG00000010072.16   22712.0\n",
       "ENSG00000009780.15   15246.0\n",
       "ENSG00000048707.15   11175.0\n",
       "ENSG00000059588.10   14109.0\n",
       "ENSG00000041988.15   17368.0\n",
       "ENSG00000049245.13   73043.0\n",
       "ENSG00000052723.11   60322.0\n",
       "ENSG00000058799.15   22188.0\n",
       "ENSG00000060642.10   18859.0\n",
       "ENSG00000069424.15    9673.0\n",
       "ENSG00000074964.17    5560.0\n",
       "ENSG00000081870.11   87432.0\n",
       "ENSG00000083444.17   39605.0\n",
       "ENSG00000076321.11   13877.0\n",
       "ENSG00000069702.11    1063.0\n",
       "ENSG00000074800.16  180479.0\n",
       "ENSG00000097046.13   12540.0\n",
       "ENSG00000097096.9     7037.0\n",
       "ENSG00000031698.13  104264.0\n",
       "ENSG00000116128.11    4346.0\n",
       "ENSG00000116205.14    6010.0\n",
       "ENSG00000116209.12  124887.0\n",
       "ENSG00000116251.11   60890.0\n",
       "ENSG00000116455.14   16696.0\n",
       "ENSG00000116667.14    2166.0\n",
       "ENSG00000116670.15   70475.0\n",
       "ENSG00000116688.16   24551.0\n",
       "ENSG00000116691.11   30275.0\n",
       "...                      ...\n",
       "ENSG00000134516.17     392.0\n",
       "ENSG00000255245.4        7.0\n",
       "ENSG00000241993.1        3.0\n",
       "ENSG00000241135.6        3.0\n",
       "ENSG00000158882.15     151.0\n",
       "ENSG00000234884.2        4.0\n",
       "ENSG00000234076.1      257.0\n",
       "ENSG00000261678.3      175.0\n",
       "ENSG00000179958.9      165.0\n",
       "ENSG00000227080.2        6.0\n",
       "ENSG00000254418.1      460.0\n",
       "ENSG00000102575.13     126.0\n",
       "ENSG00000271553.1      556.0\n",
       "ENSG00000223298.1      263.0\n",
       "ENSG00000231346.5      142.0\n",
       "ENSG00000143839.15      75.0\n",
       "ENSG00000174450.12      55.0\n",
       "ENSG00000244694.7        9.0\n",
       "ENSG00000262343.1       13.0\n",
       "ENSG00000239323.1       33.0\n",
       "ENSG00000161835.11       6.0\n",
       "ENSG00000173809.18     124.0\n",
       "ENSG00000237126.8       62.0\n",
       "ENSG00000236699.9       12.0\n",
       "ENSG00000242252.2      149.0\n",
       "ENSG00000242461.1       35.0\n",
       "ENSG00000231364.3       23.0\n",
       "ENSG00000288023.1      309.0\n",
       "ENSG00000211445.12   34066.0\n",
       "ENSG00000267547.1      631.0\n",
       "\n",
       "[22555 rows x 1 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.DataFrame(data=adata.var.apply(sum,1,result_type='reduce'),columns=['n_cells'])\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n_cells</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000001460.18</th>\n",
       "      <td>7252.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000001461.17</th>\n",
       "      <td>31838.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000010072.16</th>\n",
       "      <td>22712.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000009780.15</th>\n",
       "      <td>15246.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000048707.15</th>\n",
       "      <td>11175.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                    n_cells\n",
       "ENSG00000001460.18   7252.0\n",
       "ENSG00000001461.17  31838.0\n",
       "ENSG00000010072.16  22712.0\n",
       "ENSG00000009780.15  15246.0\n",
       "ENSG00000048707.15  11175.0"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.var = df\n",
    "adata.var.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AnnData object with n_obs × n_vars = 223413 × 22555 \n",
      "    obs: 'folder', 'n_genes'\n",
      "    var: 'n_cells'\n",
      "    layers: 'spliced', 'unspliced'\n",
      "                     folder  n_genes\n",
      "AAACCTGAGCGATTCT-0  S4_L007     2596\n",
      "AAACCTGAGCTTTGGT-0  S4_L007      329\n",
      "AAACCTGAGGCCCTCA-0  S4_L007     2178\n",
      "AAACCTGAGTAGCCGA-0  S4_L007      253\n",
      "AAACCTGGTAGCGCTC-0  S4_L007      420\n",
      "                    n_cells\n",
      "ENSG00000001460.18   7252.0\n",
      "ENSG00000001461.17  31838.0\n",
      "ENSG00000010072.16  22712.0\n",
      "ENSG00000009780.15  15246.0\n",
      "ENSG00000048707.15  11175.0\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<223413x22555 sparse matrix of type '<class 'numpy.float32'>'\n",
       "\twith 396045101 stored elements in Compressed Sparse Row format>"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(adata)\n",
    "print(adata.obs.head())\n",
    "print(adata.var.head())\n",
    "adata.layers['spliced']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "... storing 'folder' as categorical\n"
     ]
    }
   ],
   "source": [
    "adata.write('processed_adata.h5ad')"
   ]
  }
 ],
 "metadata": {
  "jupytext": {
   "formats": "ipynb,md"
  },
  "kernelspec": {
   "display_name": "(Fertig) Python 3.7",
   "language": "python",
   "name": "fertig_python_3_7"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}