generate_h5ad.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.10.9\n"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import anndata as ad\n",
    "import scanpy as sc\n",
    "import scipy.io\n",
    "from scipy.sparse import csr_matrix\n",
    "print(ad.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "counts = scipy.io.mmread('data/primary_sparse.mtx').tocsr().transpose()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "raw cell number 156572, raw gene number 25147, the dim of the raw matrix(156572, 25147), the processed gene number 25129\n"
     ]
    }
   ],
   "source": [
    "# Load barcodes and genes\n",
    "raw_barcodes = pd.read_csv('data/primary_colnames_raw.txt', header=None).squeeze().tolist()\n",
    "raw_genes = pd.read_csv('data/primary_features_raw.txt', header=None).squeeze().tolist()\n",
    "processed_genes = pd.read_csv('data/primary_features_processed.txt', header=None).squeeze().tolist()\n",
    "\n",
    "print(f\"raw cell number {len(raw_barcodes)}, raw gene number {len(raw_genes)}, the dim of the raw matrix{counts.shape}, the processed gene number {len(processed_genes)}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "adata = sc.AnnData(X=counts)\n",
    "adata.var_names = raw_genes\n",
    "adata.obs_names = raw_barcodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "25129"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.var_names.intersection(processed_genes)\n",
    "# this contains the gene only found in the processed data\n",
    "adata_corrected = adata[:, processed_genes].copy()\n",
    "len(adata_corrected.var)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/pj/g7ctw93j7477th9q941xfyyc0000gn/T/ipykernel_30998/4086199203.py:1: DtypeWarning: Columns (16,17) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  metadata = pd.read_table('data/scp_primary_metadata.txt', index_col=0)\n",
      "/var/folders/pj/g7ctw93j7477th9q941xfyyc0000gn/T/ipykernel_30998/4086199203.py:5: DtypeWarning: Columns (4,5,6) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  cluster_data = pd.read_table('data/primary_clusterdata.txt', index_col=0)\n"
     ]
    }
   ],
   "source": [
    "metadata = pd.read_table('data/scp_primary_metadata.txt', index_col=0)\n",
    "# Remove the first row\n",
    "metadata = metadata.iloc[1:]\n",
    "\n",
    "cluster_data = pd.read_table('data/primary_clusterdata.txt', index_col=0)\n",
    "# Remove the first row\n",
    "cluster_data = cluster_data.iloc[1:]\n",
    "\n",
    "combined_metadata = pd.merge(cluster_data, metadata, left_index=True, right_index=True)\n",
    "adata.obs = combined_metadata\n",
    "\n",
    "adata.obs = adata.obs.astype('category')\n",
    "\n",
    "columns_to_convert = ['X', 'Y', 'number_of_reads', 'number_of_features', 'Cell.Type']\n",
    "for column in columns_to_convert:\n",
    "    adata.obs[column] = pd.to_numeric(adata.obs[column])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>Tissue.Region</th>\n",
       "      <th>Cluster.Label</th>\n",
       "      <th>Time.Point</th>\n",
       "      <th>X</th>\n",
       "      <th>Y</th>\n",
       "      <th>Cell.Type</th>\n",
       "      <th>biosample_id</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>species</th>\n",
       "      <th>species__ontology_label</th>\n",
       "      <th>...</th>\n",
       "      <th>organ</th>\n",
       "      <th>organ__ontology_label</th>\n",
       "      <th>organ_custom</th>\n",
       "      <th>library_preparation_protocol</th>\n",
       "      <th>library_preparation_protocol__ontology_label</th>\n",
       "      <th>cell_type</th>\n",
       "      <th>cell_type__ontology_label</th>\n",
       "      <th>cell_type_custom</th>\n",
       "      <th>number_of_reads</th>\n",
       "      <th>number_of_features</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>NAME</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",
       "      <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>D14_OE.AAACCCAGTATTCCTT</th>\n",
       "      <td>OM</td>\n",
       "      <td>MT-Hi B</td>\n",
       "      <td>14 dpi</td>\n",
       "      <td>-11.398092</td>\n",
       "      <td>-1.642075</td>\n",
       "      <td>5</td>\n",
       "      <td>D14_OM</td>\n",
       "      <td>D14_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>OM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000236</td>\n",
       "      <td>B cell</td>\n",
       "      <td>MT-Hi B</td>\n",
       "      <td>1762</td>\n",
       "      <td>966</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D14_OE.AAACGAACAAAGCTCT</th>\n",
       "      <td>OM</td>\n",
       "      <td>Nme1/Nme2 Hi B</td>\n",
       "      <td>14 dpi</td>\n",
       "      <td>-13.586423</td>\n",
       "      <td>-4.545745</td>\n",
       "      <td>5</td>\n",
       "      <td>D14_OM</td>\n",
       "      <td>D14_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>OM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000236</td>\n",
       "      <td>B cell</td>\n",
       "      <td>Nme1/Nme2 Hi B</td>\n",
       "      <td>2175</td>\n",
       "      <td>969</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D14_OE.AAACGAAGTGTTAAAG</th>\n",
       "      <td>OM</td>\n",
       "      <td>Immature B</td>\n",
       "      <td>14 dpi</td>\n",
       "      <td>-11.207908</td>\n",
       "      <td>-1.848815</td>\n",
       "      <td>5</td>\n",
       "      <td>D14_OM</td>\n",
       "      <td>D14_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>OM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000236</td>\n",
       "      <td>B cell</td>\n",
       "      <td>Immature B</td>\n",
       "      <td>893</td>\n",
       "      <td>573</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D14_OE.AAACGCTAGAATACAC</th>\n",
       "      <td>OM</td>\n",
       "      <td>Immature B</td>\n",
       "      <td>14 dpi</td>\n",
       "      <td>-11.215386</td>\n",
       "      <td>-1.674733</td>\n",
       "      <td>5</td>\n",
       "      <td>D14_OM</td>\n",
       "      <td>D14_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>OM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000236</td>\n",
       "      <td>B cell</td>\n",
       "      <td>Immature B</td>\n",
       "      <td>1459</td>\n",
       "      <td>843</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D14_OE.AAACGCTAGCATCCTA</th>\n",
       "      <td>OM</td>\n",
       "      <td>Mature B 2</td>\n",
       "      <td>14 dpi</td>\n",
       "      <td>-12.391555</td>\n",
       "      <td>-4.034981</td>\n",
       "      <td>5</td>\n",
       "      <td>D14_OM</td>\n",
       "      <td>D14_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>OM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000236</td>\n",
       "      <td>B cell</td>\n",
       "      <td>Mature B 2</td>\n",
       "      <td>1210</td>\n",
       "      <td>590</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Naive_RE.CTCATGCAGGCTTAGG</th>\n",
       "      <td>RM</td>\n",
       "      <td>HSC</td>\n",
       "      <td>Naive</td>\n",
       "      <td>2.256732</td>\n",
       "      <td>-12.009367</td>\n",
       "      <td>10</td>\n",
       "      <td>Naive_RM</td>\n",
       "      <td>Naive_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>RM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000037</td>\n",
       "      <td>hematopoietic stem cell</td>\n",
       "      <td>HSC</td>\n",
       "      <td>14808</td>\n",
       "      <td>3745</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Naive_RE.GTATTGGGTGCCGGTT</th>\n",
       "      <td>RM</td>\n",
       "      <td>HSC</td>\n",
       "      <td>Naive</td>\n",
       "      <td>-5.709469</td>\n",
       "      <td>-3.818193</td>\n",
       "      <td>10</td>\n",
       "      <td>Naive_RM</td>\n",
       "      <td>Naive_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>RM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000037</td>\n",
       "      <td>hematopoietic stem cell</td>\n",
       "      <td>HSC</td>\n",
       "      <td>11051</td>\n",
       "      <td>2989</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Naive_RE.TGGGTTATCGCAATGT</th>\n",
       "      <td>RM</td>\n",
       "      <td>HSC</td>\n",
       "      <td>Naive</td>\n",
       "      <td>2.359610</td>\n",
       "      <td>-11.714253</td>\n",
       "      <td>10</td>\n",
       "      <td>Naive_RM</td>\n",
       "      <td>Naive_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0001826</td>\n",
       "      <td>nasal cavity mucosa</td>\n",
       "      <td>RM</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000037</td>\n",
       "      <td>hematopoietic stem cell</td>\n",
       "      <td>HSC</td>\n",
       "      <td>8405</td>\n",
       "      <td>2644</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Naive_LNG.AGCATCAGTGCCCAGT</th>\n",
       "      <td>LNG</td>\n",
       "      <td>HSC</td>\n",
       "      <td>Naive</td>\n",
       "      <td>-6.198734</td>\n",
       "      <td>-3.709947</td>\n",
       "      <td>10</td>\n",
       "      <td>Naive_LNG</td>\n",
       "      <td>Naive_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0035077</td>\n",
       "      <td>lateral nasal gland</td>\n",
       "      <td>LNG</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000037</td>\n",
       "      <td>hematopoietic stem cell</td>\n",
       "      <td>HSC</td>\n",
       "      <td>27226</td>\n",
       "      <td>4486</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Naive_LNG.TAACGACAGACGTCCC</th>\n",
       "      <td>LNG</td>\n",
       "      <td>HSC</td>\n",
       "      <td>Naive</td>\n",
       "      <td>2.420867</td>\n",
       "      <td>-12.134587</td>\n",
       "      <td>10</td>\n",
       "      <td>Naive_LNG</td>\n",
       "      <td>Naive_Group</td>\n",
       "      <td>NCBITaxon_10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>...</td>\n",
       "      <td>UBERON_0035077</td>\n",
       "      <td>lateral nasal gland</td>\n",
       "      <td>LNG</td>\n",
       "      <td>EFO_0009922</td>\n",
       "      <td>10x 3' v3</td>\n",
       "      <td>CL:0000037</td>\n",
       "      <td>hematopoietic stem cell</td>\n",
       "      <td>HSC</td>\n",
       "      <td>12193</td>\n",
       "      <td>2886</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>156572 rows × 23 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           Tissue.Region   Cluster.Label Time.Point  \\\n",
       "NAME                                                                  \n",
       "D14_OE.AAACCCAGTATTCCTT               OM         MT-Hi B     14 dpi   \n",
       "D14_OE.AAACGAACAAAGCTCT               OM  Nme1/Nme2 Hi B     14 dpi   \n",
       "D14_OE.AAACGAAGTGTTAAAG               OM      Immature B     14 dpi   \n",
       "D14_OE.AAACGCTAGAATACAC               OM      Immature B     14 dpi   \n",
       "D14_OE.AAACGCTAGCATCCTA               OM      Mature B 2     14 dpi   \n",
       "...                                  ...             ...        ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG             RM             HSC      Naive   \n",
       "Naive_RE.GTATTGGGTGCCGGTT             RM             HSC      Naive   \n",
       "Naive_RE.TGGGTTATCGCAATGT             RM             HSC      Naive   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT           LNG             HSC      Naive   \n",
       "Naive_LNG.TAACGACAGACGTCCC           LNG             HSC      Naive   \n",
       "\n",
       "                                    X          Y  Cell.Type biosample_id  \\\n",
       "NAME                                                                       \n",
       "D14_OE.AAACCCAGTATTCCTT    -11.398092  -1.642075          5       D14_OM   \n",
       "D14_OE.AAACGAACAAAGCTCT    -13.586423  -4.545745          5       D14_OM   \n",
       "D14_OE.AAACGAAGTGTTAAAG    -11.207908  -1.848815          5       D14_OM   \n",
       "D14_OE.AAACGCTAGAATACAC    -11.215386  -1.674733          5       D14_OM   \n",
       "D14_OE.AAACGCTAGCATCCTA    -12.391555  -4.034981          5       D14_OM   \n",
       "...                               ...        ...        ...          ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG    2.256732 -12.009367         10     Naive_RM   \n",
       "Naive_RE.GTATTGGGTGCCGGTT   -5.709469  -3.818193         10     Naive_RM   \n",
       "Naive_RE.TGGGTTATCGCAATGT    2.359610 -11.714253         10     Naive_RM   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT  -6.198734  -3.709947         10    Naive_LNG   \n",
       "Naive_LNG.TAACGACAGACGTCCC   2.420867 -12.134587         10    Naive_LNG   \n",
       "\n",
       "                               donor_id          species  \\\n",
       "NAME                                                       \n",
       "D14_OE.AAACCCAGTATTCCTT       D14_Group  NCBITaxon_10090   \n",
       "D14_OE.AAACGAACAAAGCTCT       D14_Group  NCBITaxon_10090   \n",
       "D14_OE.AAACGAAGTGTTAAAG       D14_Group  NCBITaxon_10090   \n",
       "D14_OE.AAACGCTAGAATACAC       D14_Group  NCBITaxon_10090   \n",
       "D14_OE.AAACGCTAGCATCCTA       D14_Group  NCBITaxon_10090   \n",
       "...                                 ...              ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG   Naive_Group  NCBITaxon_10090   \n",
       "Naive_RE.GTATTGGGTGCCGGTT   Naive_Group  NCBITaxon_10090   \n",
       "Naive_RE.TGGGTTATCGCAATGT   Naive_Group  NCBITaxon_10090   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT  Naive_Group  NCBITaxon_10090   \n",
       "Naive_LNG.TAACGACAGACGTCCC  Naive_Group  NCBITaxon_10090   \n",
       "\n",
       "                           species__ontology_label  ...           organ  \\\n",
       "NAME                                                ...                   \n",
       "D14_OE.AAACCCAGTATTCCTT               Mus musculus  ...  UBERON_0001826   \n",
       "D14_OE.AAACGAACAAAGCTCT               Mus musculus  ...  UBERON_0001826   \n",
       "D14_OE.AAACGAAGTGTTAAAG               Mus musculus  ...  UBERON_0001826   \n",
       "D14_OE.AAACGCTAGAATACAC               Mus musculus  ...  UBERON_0001826   \n",
       "D14_OE.AAACGCTAGCATCCTA               Mus musculus  ...  UBERON_0001826   \n",
       "...                                            ...  ...             ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG             Mus musculus  ...  UBERON_0001826   \n",
       "Naive_RE.GTATTGGGTGCCGGTT             Mus musculus  ...  UBERON_0001826   \n",
       "Naive_RE.TGGGTTATCGCAATGT             Mus musculus  ...  UBERON_0001826   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT            Mus musculus  ...  UBERON_0035077   \n",
       "Naive_LNG.TAACGACAGACGTCCC            Mus musculus  ...  UBERON_0035077   \n",
       "\n",
       "                           organ__ontology_label organ_custom  \\\n",
       "NAME                                                            \n",
       "D14_OE.AAACCCAGTATTCCTT      nasal cavity mucosa           OM   \n",
       "D14_OE.AAACGAACAAAGCTCT      nasal cavity mucosa           OM   \n",
       "D14_OE.AAACGAAGTGTTAAAG      nasal cavity mucosa           OM   \n",
       "D14_OE.AAACGCTAGAATACAC      nasal cavity mucosa           OM   \n",
       "D14_OE.AAACGCTAGCATCCTA      nasal cavity mucosa           OM   \n",
       "...                                          ...          ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG    nasal cavity mucosa           RM   \n",
       "Naive_RE.GTATTGGGTGCCGGTT    nasal cavity mucosa           RM   \n",
       "Naive_RE.TGGGTTATCGCAATGT    nasal cavity mucosa           RM   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT   lateral nasal gland          LNG   \n",
       "Naive_LNG.TAACGACAGACGTCCC   lateral nasal gland          LNG   \n",
       "\n",
       "                           library_preparation_protocol  \\\n",
       "NAME                                                      \n",
       "D14_OE.AAACCCAGTATTCCTT                     EFO_0009922   \n",
       "D14_OE.AAACGAACAAAGCTCT                     EFO_0009922   \n",
       "D14_OE.AAACGAAGTGTTAAAG                     EFO_0009922   \n",
       "D14_OE.AAACGCTAGAATACAC                     EFO_0009922   \n",
       "D14_OE.AAACGCTAGCATCCTA                     EFO_0009922   \n",
       "...                                                 ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG                   EFO_0009922   \n",
       "Naive_RE.GTATTGGGTGCCGGTT                   EFO_0009922   \n",
       "Naive_RE.TGGGTTATCGCAATGT                   EFO_0009922   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT                  EFO_0009922   \n",
       "Naive_LNG.TAACGACAGACGTCCC                  EFO_0009922   \n",
       "\n",
       "                           library_preparation_protocol__ontology_label  \\\n",
       "NAME                                                                      \n",
       "D14_OE.AAACCCAGTATTCCTT                                       10x 3' v3   \n",
       "D14_OE.AAACGAACAAAGCTCT                                       10x 3' v3   \n",
       "D14_OE.AAACGAAGTGTTAAAG                                       10x 3' v3   \n",
       "D14_OE.AAACGCTAGAATACAC                                       10x 3' v3   \n",
       "D14_OE.AAACGCTAGCATCCTA                                       10x 3' v3   \n",
       "...                                                                 ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG                                     10x 3' v3   \n",
       "Naive_RE.GTATTGGGTGCCGGTT                                     10x 3' v3   \n",
       "Naive_RE.TGGGTTATCGCAATGT                                     10x 3' v3   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT                                    10x 3' v3   \n",
       "Naive_LNG.TAACGACAGACGTCCC                                    10x 3' v3   \n",
       "\n",
       "                             cell_type cell_type__ontology_label  \\\n",
       "NAME                                                               \n",
       "D14_OE.AAACCCAGTATTCCTT     CL:0000236                    B cell   \n",
       "D14_OE.AAACGAACAAAGCTCT     CL:0000236                    B cell   \n",
       "D14_OE.AAACGAAGTGTTAAAG     CL:0000236                    B cell   \n",
       "D14_OE.AAACGCTAGAATACAC     CL:0000236                    B cell   \n",
       "D14_OE.AAACGCTAGCATCCTA     CL:0000236                    B cell   \n",
       "...                                ...                       ...   \n",
       "Naive_RE.CTCATGCAGGCTTAGG   CL:0000037   hematopoietic stem cell   \n",
       "Naive_RE.GTATTGGGTGCCGGTT   CL:0000037   hematopoietic stem cell   \n",
       "Naive_RE.TGGGTTATCGCAATGT   CL:0000037   hematopoietic stem cell   \n",
       "Naive_LNG.AGCATCAGTGCCCAGT  CL:0000037   hematopoietic stem cell   \n",
       "Naive_LNG.TAACGACAGACGTCCC  CL:0000037   hematopoietic stem cell   \n",
       "\n",
       "                           cell_type_custom number_of_reads number_of_features  \n",
       "NAME                                                                            \n",
       "D14_OE.AAACCCAGTATTCCTT             MT-Hi B            1762                966  \n",
       "D14_OE.AAACGAACAAAGCTCT      Nme1/Nme2 Hi B            2175                969  \n",
       "D14_OE.AAACGAAGTGTTAAAG          Immature B             893                573  \n",
       "D14_OE.AAACGCTAGAATACAC          Immature B            1459                843  \n",
       "D14_OE.AAACGCTAGCATCCTA          Mature B 2            1210                590  \n",
       "...                                     ...             ...                ...  \n",
       "Naive_RE.CTCATGCAGGCTTAGG               HSC           14808               3745  \n",
       "Naive_RE.GTATTGGGTGCCGGTT               HSC           11051               2989  \n",
       "Naive_RE.TGGGTTATCGCAATGT               HSC            8405               2644  \n",
       "Naive_LNG.AGCATCAGTGCCCAGT              HSC           27226               4486  \n",
       "Naive_LNG.TAACGACAGACGTCCC              HSC           12193               2886  \n",
       "\n",
       "[156572 rows x 23 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.obs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "ename": "",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31mThe Kernel crashed while executing code in the current cell or a previous cell. \n",
      "\u001b[1;31mPlease review the code in the cell(s) to identify a possible cause of the failure. \n",
      "\u001b[1;31mClick <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. \n",
      "\u001b[1;31mView Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
     ]
    }
   ],
   "source": [
    "# need to be float for BPCells, otherwise you gonna spend 2hr debugging it\n",
    "adata_corrected.X = adata_corrected.X.astype(np.float64)\n",
    "\n",
    "adata_corrected.write('data/flu_raw.h5ad', compression=\"gzip\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "adata_corrected.X.dtype\n"
   ]
  }
 ],
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