scRNA_subsetting.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "749b9b9c-0099-4de3-bcea-6d2c5ea56d72",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-------------------original data--------------------------\n",
      "-------------------tissue categories----------------------\n",
      "Index(['Aorta', 'BAT', 'Bladder', 'Brain_Myeloid', 'Brain_Non-Myeloid',\n",
      "       'Diaphragm', 'GAT', 'Heart', 'Kidney', 'Large_Intestine', 'Limb_Muscle',\n",
      "       'Liver', 'Lung', 'MAT', 'Mammary_Gland', 'Marrow', 'Pancreas', 'SCAT',\n",
      "       'Skin', 'Spleen', 'Thymus', 'Tongue', 'Trachea'],\n",
      "      dtype='object')\n",
      "-------------------age categories-------------------------\n",
      "Index(['3m', '18m', '21m', '24m'], dtype='object')\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/hsieh/opt/anaconda3/lib/python3.9/site-packages/anndata/compat/__init__.py:232: FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances'].\n",
      "\n",
      "This is where adjacency matrices should go now.\n",
      "  warn(\n",
      "/Users/hsieh/opt/anaconda3/lib/python3.9/site-packages/anndata/compat/__init__.py:232: FutureWarning: Moving element from .uns['neighbors']['connectivities'] to .obsp['connectivities'].\n",
      "\n",
      "This is where adjacency matrices should go now.\n",
      "  warn(\n"
     ]
    },
    {
     "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>FACS.selection</th>\n",
       "      <th>age</th>\n",
       "      <th>cell</th>\n",
       "      <th>cell_ontology_class</th>\n",
       "      <th>cell_ontology_id</th>\n",
       "      <th>free_annotation</th>\n",
       "      <th>method</th>\n",
       "      <th>mouse.id</th>\n",
       "      <th>sex</th>\n",
       "      <th>subtissue</th>\n",
       "      <th>tissue</th>\n",
       "      <th>n_genes</th>\n",
       "      <th>n_counts</th>\n",
       "      <th>louvain</th>\n",
       "      <th>leiden</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>index</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>A10_B000497_B009023_S10.mm10-plus-0-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B000497</td>\n",
       "      <td>bulge keratinocyte</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>nan</td>\n",
       "      <td>Skin</td>\n",
       "      <td>2706</td>\n",
       "      <td>1009830.0</td>\n",
       "      <td>10</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B000756_B007446_S10.mm10-plus-0-0</th>\n",
       "      <td>Viable</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B000756</td>\n",
       "      <td>pancreatic B cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>pancreatic B cell</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_45_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Endocrine</td>\n",
       "      <td>Pancreas</td>\n",
       "      <td>3212</td>\n",
       "      <td>978772.0</td>\n",
       "      <td>31</td>\n",
       "      <td>27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B000802_B009022_S10.mm10-plus-0-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B000802</td>\n",
       "      <td>bulge keratinocyte</td>\n",
       "      <td>nan</td>\n",
       "      <td>outer bulge</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_47_F</td>\n",
       "      <td>female</td>\n",
       "      <td>Skin Anagen</td>\n",
       "      <td>Skin</td>\n",
       "      <td>2243</td>\n",
       "      <td>419722.0</td>\n",
       "      <td>10</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B000927_B007456_S10.mm10-plus-0-0</th>\n",
       "      <td>CD31+, CD45+, CD31-CD45-Sca1+, CD31-CD45-Sca1-...</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B000927</td>\n",
       "      <td>skeletal muscle satellite cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_46_F</td>\n",
       "      <td>female</td>\n",
       "      <td>Muscle Diaphragm</td>\n",
       "      <td>Limb_Muscle</td>\n",
       "      <td>2789</td>\n",
       "      <td>878950.0</td>\n",
       "      <td>12</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B001361_B007505_S10.mm10-plus-0-0</th>\n",
       "      <td>Viable</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B001361</td>\n",
       "      <td>B cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>B cell</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_46_F</td>\n",
       "      <td>female</td>\n",
       "      <td>RV</td>\n",
       "      <td>Heart</td>\n",
       "      <td>1237</td>\n",
       "      <td>6587.0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B002452_B009020_S10.mm10-plus-0-0</th>\n",
       "      <td>Viable</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B002452</td>\n",
       "      <td>B cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>CD79a B cell</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_47_F</td>\n",
       "      <td>female</td>\n",
       "      <td>nan</td>\n",
       "      <td>Spleen</td>\n",
       "      <td>2178</td>\n",
       "      <td>1794279.0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B002850_B007342_S10.mm10-plus-0-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B002850</td>\n",
       "      <td>bulge keratinocyte</td>\n",
       "      <td>nan</td>\n",
       "      <td>outer bulge</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_47_F</td>\n",
       "      <td>female</td>\n",
       "      <td>nan</td>\n",
       "      <td>Skin</td>\n",
       "      <td>3731</td>\n",
       "      <td>1734592.0</td>\n",
       "      <td>10</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B003262_B007459_S10.mm10-plus-0-0</th>\n",
       "      <td>CD31+, CD45+, CD31-CD45-Sca1+, CD31-CD45-Sca1-...</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B003262</td>\n",
       "      <td>skeletal muscle satellite cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_45_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Limb_Muscle</td>\n",
       "      <td>Diaphragm</td>\n",
       "      <td>1089</td>\n",
       "      <td>1426060.0</td>\n",
       "      <td>12</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A10_B003294_B007450_S10.mm10-plus-0-0</th>\n",
       "      <td>CD31+, CD45+, CD31-CD45-Sca1+, CD31-CD45-Sca1-...</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B003294</td>\n",
       "      <td>skeletal muscle satellite cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_47_F</td>\n",
       "      <td>female</td>\n",
       "      <td>Muscle forelimb and hindlimb</td>\n",
       "      <td>Limb_Muscle</td>\n",
       "      <td>1838</td>\n",
       "      <td>1775407.0</td>\n",
       "      <td>12</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A11_B000497_B009023_S11.mm10-plus-0-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A11_B000497</td>\n",
       "      <td>bulge keratinocyte</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>nan</td>\n",
       "      <td>Skin</td>\n",
       "      <td>2186</td>\n",
       "      <td>496482.0</td>\n",
       "      <td>10</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                                          FACS.selection  \\\n",
       "index                                                                                      \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0                                           Multiple   \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0                                             Viable   \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0                                           Multiple   \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0  CD31+, CD45+, CD31-CD45-Sca1+, CD31-CD45-Sca1-...   \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0                                             Viable   \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0                                             Viable   \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0                                           Multiple   \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0  CD31+, CD45+, CD31-CD45-Sca1+, CD31-CD45-Sca1-...   \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0  CD31+, CD45+, CD31-CD45-Sca1+, CD31-CD45-Sca1-...   \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0                                           Multiple   \n",
       "\n",
       "                                       age         cell  \\\n",
       "index                                                     \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0  18m  A10_B000497   \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0  18m  A10_B000756   \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0  18m  A10_B000802   \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0  18m  A10_B000927   \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0  18m  A10_B001361   \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0  18m  A10_B002452   \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0  18m  A10_B002850   \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0  18m  A10_B003262   \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0  18m  A10_B003294   \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0  18m  A11_B000497   \n",
       "\n",
       "                                                  cell_ontology_class  \\\n",
       "index                                                                   \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0              bulge keratinocyte   \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0               pancreatic B cell   \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0              bulge keratinocyte   \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0  skeletal muscle satellite cell   \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0                          B cell   \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0                          B cell   \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0              bulge keratinocyte   \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0  skeletal muscle satellite cell   \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0  skeletal muscle satellite cell   \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0              bulge keratinocyte   \n",
       "\n",
       "                                      cell_ontology_id    free_annotation  \\\n",
       "index                                                                       \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0              nan                nan   \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0              nan  pancreatic B cell   \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0              nan        outer bulge   \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0              nan                nan   \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0              nan             B cell   \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0              nan       CD79a B cell   \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0              nan        outer bulge   \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0              nan                nan   \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0              nan                nan   \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0              nan                nan   \n",
       "\n",
       "                                      method mouse.id     sex  \\\n",
       "index                                                           \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0   facs  18_53_M    male   \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0   facs  18_45_M    male   \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0   facs  18_47_F  female   \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0   facs  18_46_F  female   \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0   facs  18_46_F  female   \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0   facs  18_47_F  female   \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0   facs  18_47_F  female   \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0   facs  18_45_M    male   \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0   facs  18_47_F  female   \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0   facs  18_53_M    male   \n",
       "\n",
       "                                                          subtissue  \\\n",
       "index                                                                 \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0                           nan   \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0                     Endocrine   \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0                   Skin Anagen   \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0              Muscle Diaphragm   \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0                            RV   \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0                           nan   \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0                           nan   \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0                   Limb_Muscle   \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0  Muscle forelimb and hindlimb   \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0                           nan   \n",
       "\n",
       "                                            tissue  n_genes   n_counts  \\\n",
       "index                                                                    \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0         Skin     2706  1009830.0   \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0     Pancreas     3212   978772.0   \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0         Skin     2243   419722.0   \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0  Limb_Muscle     2789   878950.0   \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0        Heart     1237     6587.0   \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0       Spleen     2178  1794279.0   \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0         Skin     3731  1734592.0   \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0    Diaphragm     1089  1426060.0   \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0  Limb_Muscle     1838  1775407.0   \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0         Skin     2186   496482.0   \n",
       "\n",
       "                                      louvain leiden  \n",
       "index                                                 \n",
       "A10_B000497_B009023_S10.mm10-plus-0-0      10      9  \n",
       "A10_B000756_B007446_S10.mm10-plus-0-0      31     27  \n",
       "A10_B000802_B009022_S10.mm10-plus-0-0      10      9  \n",
       "A10_B000927_B007456_S10.mm10-plus-0-0      12     11  \n",
       "A10_B001361_B007505_S10.mm10-plus-0-0       1      1  \n",
       "A10_B002452_B009020_S10.mm10-plus-0-0       1      1  \n",
       "A10_B002850_B007342_S10.mm10-plus-0-0      10      9  \n",
       "A10_B003262_B007459_S10.mm10-plus-0-0      12     11  \n",
       "A10_B003294_B007450_S10.mm10-plus-0-0      12     11  \n",
       "A11_B000497_B009023_S11.mm10-plus-0-0      10      9  "
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Packages\n",
    "import os, sys\n",
    "import scanpy as sc\n",
    "import anndata\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "from pathlib import Path\n",
    "%matplotlib inline\n",
    "\n",
    "# Dir\n",
    "dir = os.getcwd()\n",
    "subset = 'subset'\n",
    "droplet = 'tabula-muris-senis-droplet-processed-official-annotations.h5ad'\n",
    "facs = 'tabula-muris-senis-facs-processed-official-annotations.h5ad'\n",
    "fn_droplet = Path(dir, droplet)\n",
    "fn_facs = Path(dir, facs)\n",
    "subset_dir = Path(dir,subset)\n",
    "\n",
    "# Set variables\n",
    "# method = 'droplet'\n",
    "method = 'facs'\n",
    "GroupBy = 'age'\n",
    "\n",
    "# Read data and subsetting it\n",
    "# adata = sc.read_h5ad(fn_droplet)\n",
    "adata = sc.read_h5ad(fn_facs)\n",
    "\n",
    "# Check how many categories in selected variables\n",
    "df_obs = pd.DataFrame(adata.obs)\n",
    "print(\"-------------------original data--------------------------\")\n",
    "print(\"-------------------tissue categories----------------------\")\n",
    "print(df_obs['tissue'].cat.categories)\n",
    "print(\"-------------------age categories-------------------------\")\n",
    "print(df_obs['age'].cat.categories)\n",
    "\n",
    "# View the annotations\n",
    "adata.obs[:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "095b993f-54b5-4e52-a6c5-de6fd0ef98bc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-------------------subsetted data--------------------------\n",
      "-------------------tissue categories---------------------- \n",
      "Index(['Large_Intestine'], dtype='object')\n",
      "-------------------age categories------------------------- \n",
      "Index(['3m', '18m', '24m'], dtype='object')\n",
      "-------------------cell ontology categories--------------- \n",
      "Index(['Brush cell of epithelium proper of large intestine',\n",
      "       'enterocyte of epithelium of large intestine', 'enteroendocrine cell',\n",
      "       'epithelial cell of large intestine', 'intestinal crypt stem cell',\n",
      "       'large intestine goblet cell', 'secretory cell'],\n",
      "      dtype='object')\n"
     ]
    }
   ],
   "source": [
    "# Subset data from large intestine\n",
    "Tissue = ['Large_Intestine']\n",
    "adata_subset = adata[adata.obs['tissue'].isin(Tissue)]\n",
    "\n",
    "print(\"-------------------subsetted data--------------------------\")\n",
    "df_subset_obs = pd.DataFrame(adata_subset.obs)\n",
    "print(\"-------------------tissue categories---------------------- \")\n",
    "print(df_subset_obs['tissue'].cat.categories)\n",
    "print(\"-------------------age categories------------------------- \")\n",
    "print(df_subset_obs['age'].cat.categories)\n",
    "print(\"-------------------cell ontology categories--------------- \")\n",
    "print(df_subset_obs['cell_ontology_class'].cat.categories)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "24a6b934",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/hsieh/opt/anaconda3/lib/python3.9/site-packages/scanpy/preprocessing/_simple.py:140: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
      "  adata.obs['n_genes'] = number\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AnnData object with n_obs × n_vars = 8311 × 22075\n",
      "    obs: 'FACS.selection', 'age', 'cell', 'cell_ontology_class', 'cell_ontology_id', 'free_annotation', 'method', 'mouse.id', 'sex', 'subtissue', 'tissue', 'n_genes', 'n_counts', 'louvain', 'leiden'\n",
      "    var: 'n_cells', 'means', 'dispersions', 'dispersions_norm', 'highly_variable'\n",
      "    uns: 'leiden', 'louvain', 'louvain_colors', 'neighbors', 'pca', 'tissue_colors'\n",
      "    obsm: 'X_pca', 'X_umap'\n",
      "    varm: 'PCs'\n",
      "    obsp: 'distances', 'connectivities'\n"
     ]
    }
   ],
   "source": [
    "# Filter cells\n",
    "sc.pp.filter_cells(adata_subset, min_genes=200)\n",
    "sc.pp.filter_genes(adata_subset, min_cells=3)\n",
    "print(adata_subset)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "6f08de8b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# normalize the expression, the unit is CPM (counts per million)\n",
    "# but for DESeq, don't normalize the data\n",
    "# sc.pp.normalize_total(adata_subset, target_sum=1e6)\n",
    "\n",
    "# log transform the raw data\n",
    "# and set the 'raw' attribute to the natural logarithmized data\n",
    "sc.pp.log1p(adata_subset)\n",
    "\n",
    "# Freeze the data in log transform value\n",
    "adata_subset.raw = adata_subset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "315e859d",
   "metadata": {},
   "outputs": [
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       "index                                  0610005C13Rik  0610007C21Rik  \\\n",
       "index                                                                 \n",
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       "\n",
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       "index                                                                 \n",
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       "\n",
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       "index                                                                 \n",
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       "A18_B000246_B008313_S18.mm10-plus-3-0       0.000000       1.368265   \n",
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       "\n",
       "index                                  0610007P22Rik  0610008F07Rik  \\\n",
       "index                                                                 \n",
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       "A18_B000246_B008313_S18.mm10-plus-3-0       1.219583            0.0   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0       0.000000            0.0   \n",
       "\n",
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       "index                                                                ...   \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0            0.0       1.006562  ...   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0            0.0       0.000000  ...   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0            0.0       0.496369  ...   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0            0.0       0.000000  ...   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0            0.0       0.265976  ...   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0            0.0       0.000000  ...   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0            0.0       0.404960  ...   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0            0.0       0.705291  ...   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0            0.0       0.000000  ...   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0            0.0       0.000000  ...   \n",
       "\n",
       "index                                  Zwilch     Zwint  Zxda  Zxdb  Zxdc  \\\n",
       "index                                                                       \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0     0.0  0.961622   0.0   0.0   0.0   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0     0.0  0.000000   0.0   0.0   0.0   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0     0.0  0.089754   0.0   0.0   0.0   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0     0.0  0.588286   0.0   0.0   0.0   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0     0.0  0.000000   0.0   0.0   0.0   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0     0.0  0.000000   0.0   0.0   0.0   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0     0.0  0.000000   0.0   0.0   0.0   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0     0.0  0.000000   0.0   0.0   0.0   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0     0.0  0.519365   0.0   0.0   0.0   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0     0.0  0.000000   0.0   0.0   0.0   \n",
       "\n",
       "index                                  Zyg11a    Zyg11b       Zyx     Zzef1  \\\n",
       "index                                                                         \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0     0.0  0.000000  0.000000  1.238606   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0     0.0  0.000000  0.031256  0.000000   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0     0.0  0.612044  0.446904  0.000000   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0     0.0  0.957936  0.000000  0.354677   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0     0.0  1.424055  0.000000  1.177988   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0     0.0  0.000000  0.147145  0.000000   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0     0.0  0.000000  0.000000  0.964368   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0     0.0  0.953433  0.032829  0.000000   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0     0.0  0.000000  0.000000  0.000000   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0     0.0  0.740390  0.000000  0.246226   \n",
       "\n",
       "index                                      Zzz3  \n",
       "index                                            \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0  0.265015  \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0  0.000000  \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0  0.000000  \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0  0.000000  \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0  0.883137  \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0  0.000000  \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0  0.000000  \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0  0.000000  \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0  0.000000  \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0  0.000000  \n",
       "\n",
       "[10 rows x 22075 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# transform the count matrix to data frame\n",
    "adata_subset.layers[\"normalized_data\"] = adata_subset.X\n",
    "df_adata_subset = adata_subset.to_df(layer=\"normalized_data\")\n",
    "\n",
    "# Take a look at the matrix data\n",
    "df_adata_subset.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "85bc3df3",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<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>FACS.selection</th>\n",
       "      <th>age</th>\n",
       "      <th>cell</th>\n",
       "      <th>cell_ontology_class</th>\n",
       "      <th>cell_ontology_id</th>\n",
       "      <th>free_annotation</th>\n",
       "      <th>method</th>\n",
       "      <th>mouse.id</th>\n",
       "      <th>sex</th>\n",
       "      <th>subtissue</th>\n",
       "      <th>tissue</th>\n",
       "      <th>n_genes</th>\n",
       "      <th>n_counts</th>\n",
       "      <th>louvain</th>\n",
       "      <th>leiden</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>index</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>A10_B000246_B008313_S10.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A10_B000246</td>\n",
       "      <td>intestinal crypt stem cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>Lgr5+ undifferentiated cell (Distal)</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>4630</td>\n",
       "      <td>950997.0</td>\n",
       "      <td>20</td>\n",
       "      <td>14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A11_B000246_B008313_S11.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A11_B000246</td>\n",
       "      <td>enteroendocrine cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>883</td>\n",
       "      <td>789856.0</td>\n",
       "      <td>11</td>\n",
       "      <td>24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A12_B000762_B008314_S12.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A12_B000762</td>\n",
       "      <td>intestinal crypt stem cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_45_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>6276</td>\n",
       "      <td>1235270.0</td>\n",
       "      <td>20</td>\n",
       "      <td>14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A13_B000762_B008314_S13.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A13_B000762</td>\n",
       "      <td>enterocyte of epithelium of large intestine</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_45_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>4299</td>\n",
       "      <td>160456.0</td>\n",
       "      <td>23</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A14_B000246_B008313_S14.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A14_B000246</td>\n",
       "      <td>enterocyte of epithelium of large intestine</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>3626</td>\n",
       "      <td>285334.0</td>\n",
       "      <td>23</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A16_B000246_B008313_S16.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A16_B000246</td>\n",
       "      <td>enterocyte of epithelium of large intestine</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>625</td>\n",
       "      <td>300802.0</td>\n",
       "      <td>23</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A17_B000246_B008313_S17.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A17_B000246</td>\n",
       "      <td>large intestine goblet cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>Goblet cell, top of crypt (Distal)</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>1835</td>\n",
       "      <td>618055.0</td>\n",
       "      <td>15</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A17_B000762_B008314_S17.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A17_B000762</td>\n",
       "      <td>enterocyte of epithelium of large intestine</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_45_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>4066</td>\n",
       "      <td>750946.0</td>\n",
       "      <td>23</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A18_B000246_B008313_S18.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A18_B000246</td>\n",
       "      <td>large intestine goblet cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_53_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>4672</td>\n",
       "      <td>1291135.0</td>\n",
       "      <td>15</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A18_B000762_B008314_S18.mm10-plus-3-0</th>\n",
       "      <td>Multiple</td>\n",
       "      <td>18m</td>\n",
       "      <td>A18_B000762</td>\n",
       "      <td>large intestine goblet cell</td>\n",
       "      <td>nan</td>\n",
       "      <td>Goblet cell, top of crypt (Distal)</td>\n",
       "      <td>facs</td>\n",
       "      <td>18_45_M</td>\n",
       "      <td>male</td>\n",
       "      <td>Distal</td>\n",
       "      <td>Large_Intestine</td>\n",
       "      <td>1931</td>\n",
       "      <td>420286.0</td>\n",
       "      <td>15</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                      FACS.selection  age         cell  \\\n",
       "index                                                                    \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0       Multiple  18m  A10_B000246   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0       Multiple  18m  A11_B000246   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0       Multiple  18m  A12_B000762   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0       Multiple  18m  A13_B000762   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0       Multiple  18m  A14_B000246   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0       Multiple  18m  A16_B000246   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0       Multiple  18m  A17_B000246   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0       Multiple  18m  A17_B000762   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0       Multiple  18m  A18_B000246   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0       Multiple  18m  A18_B000762   \n",
       "\n",
       "                                                               cell_ontology_class  \\\n",
       "index                                                                                \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0                   intestinal crypt stem cell   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0                         enteroendocrine cell   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0                   intestinal crypt stem cell   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0  enterocyte of epithelium of large intestine   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0  enterocyte of epithelium of large intestine   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0  enterocyte of epithelium of large intestine   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0                  large intestine goblet cell   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0  enterocyte of epithelium of large intestine   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0                  large intestine goblet cell   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0                  large intestine goblet cell   \n",
       "\n",
       "                                      cell_ontology_id  \\\n",
       "index                                                    \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0              nan   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0              nan   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0              nan   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0              nan   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0              nan   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0              nan   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0              nan   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0              nan   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0              nan   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0              nan   \n",
       "\n",
       "                                                            free_annotation  \\\n",
       "index                                                                         \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0  Lgr5+ undifferentiated cell (Distal)   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0                                   nan   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0                                   nan   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0                                   nan   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0                                   nan   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0                                   nan   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0    Goblet cell, top of crypt (Distal)   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0                                   nan   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0                                   nan   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0    Goblet cell, top of crypt (Distal)   \n",
       "\n",
       "                                      method mouse.id   sex subtissue  \\\n",
       "index                                                                   \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0   facs  18_53_M  male    Distal   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0   facs  18_53_M  male    Distal   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0   facs  18_45_M  male    Distal   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0   facs  18_45_M  male    Distal   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0   facs  18_53_M  male    Distal   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0   facs  18_53_M  male    Distal   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0   facs  18_53_M  male    Distal   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0   facs  18_45_M  male    Distal   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0   facs  18_53_M  male    Distal   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0   facs  18_45_M  male    Distal   \n",
       "\n",
       "                                                tissue  n_genes   n_counts  \\\n",
       "index                                                                        \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0  Large_Intestine     4630   950997.0   \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0  Large_Intestine      883   789856.0   \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0  Large_Intestine     6276  1235270.0   \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0  Large_Intestine     4299   160456.0   \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0  Large_Intestine     3626   285334.0   \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0  Large_Intestine      625   300802.0   \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0  Large_Intestine     1835   618055.0   \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0  Large_Intestine     4066   750946.0   \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0  Large_Intestine     4672  1291135.0   \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0  Large_Intestine     1931   420286.0   \n",
       "\n",
       "                                      louvain leiden  \n",
       "index                                                 \n",
       "A10_B000246_B008313_S10.mm10-plus-3-0      20     14  \n",
       "A11_B000246_B008313_S11.mm10-plus-3-0      11     24  \n",
       "A12_B000762_B008314_S12.mm10-plus-3-0      20     14  \n",
       "A13_B000762_B008314_S13.mm10-plus-3-0      23     22  \n",
       "A14_B000246_B008313_S14.mm10-plus-3-0      23     22  \n",
       "A16_B000246_B008313_S16.mm10-plus-3-0      23     22  \n",
       "A17_B000246_B008313_S17.mm10-plus-3-0      15     15  \n",
       "A17_B000762_B008314_S17.mm10-plus-3-0      23     22  \n",
       "A18_B000246_B008313_S18.mm10-plus-3-0      15     15  \n",
       "A18_B000762_B008314_S18.mm10-plus-3-0      15     15  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Transform annotation to data frame\n",
    "df_obs_subset = pd.DataFrame(adata_subset.obs)\n",
    "df_obs_subset.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "bb68c7d9",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Save subsetted count matrix and annotation data frame into csv files\n",
    "tissue_subset = 'LargeIntestine'\n",
    "annot_name=method+'_'+tissue_subset+'_'+'annot'+'.csv'\n",
    "mtx_name=method+'_'+tissue_subset+'_'+'mtx'+'.csv'\n",
    "df_obs_subset.to_csv(Path(subset,annot_name), sep=',')\n",
    "df_adata_subset.to_csv(Path(subset,mtx_name), sep=',')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fc7d3287",
   "metadata": {},
   "outputs": [],
   "source": [
    "# End"
   ]
  }
 ],
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