convert_counts_to_adata.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "c4fa34ca-5847-4d3c-a54a-ae1b78474940",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from anndata import AnnData\n",
    "from scipy.sparse import csr_matrix\n",
    "import scanpy as sc\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "e45ead5c-f2ff-42ba-af77-1dd2d1a6a517",
   "metadata": {},
   "outputs": [],
   "source": [
    "RNA = pd.read_table('AML1026_1_count_matrix_f100.txt.gz',index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8e5a6e3b-f359-4711-85d3-63dbd586e71c",
   "metadata": {},
   "outputs": [],
   "source": [
    "RNA_bygenes = RNA.T"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "75026233-804f-474d-9d19-a6110e474ac3",
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>barcode</th>\n",
       "      <th>AACAACCTAAAGACTGGT</th>\n",
       "      <th>AACAACCTAAAGTCATGA</th>\n",
       "      <th>AACAACCTACAGTATGAT</th>\n",
       "      <th>AACAACCTACATCGAAGC</th>\n",
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       "      <th>AACAACCTAGCGAAGCTC</th>\n",
       "      <th>AACAACCTATAGAGCCAG</th>\n",
       "      <th>...</th>\n",
       "      <th>TTGTCAACCTGTAACAGT</th>\n",
       "      <th>TTGTCAACCTTGATCGTA</th>\n",
       "      <th>TTGTTAGAGACGCTAGTG</th>\n",
       "      <th>TTGTTAGAGATTCGAAGA</th>\n",
       "      <th>TTGTTAGAGCAACGATCG</th>\n",
       "      <th>TTGTTAGAGCCGCTATCC</th>\n",
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       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ABHD17A_2</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>ABHD17C_1</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ZRSR2_2</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>1</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ZWINT_1</th>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>8</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ZWINT_2</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "      <td>2</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>2342 rows × 17267 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "barcode    AACAACCTAAAGACTGGT  AACAACCTAAAGTCATGA  AACAACCTACAGTATGAT  \\\n",
       "ABCE1_1                     2                   3                   4   \n",
       "ABCE1_2                     0                   0                   0   \n",
       "ABHD17A_1                   1                   0                   1   \n",
       "ABHD17A_2                   0                   0                   0   \n",
       "ABHD17C_1                   0                   0                   0   \n",
       "...                       ...                 ...                 ...   \n",
       "ZP3_2                       0                   0                   0   \n",
       "ZRSR2_1                     1                   0                   0   \n",
       "ZRSR2_2                     0                   1                   0   \n",
       "ZWINT_1                     0                   5                   1   \n",
       "ZWINT_2                     0                   0                   1   \n",
       "\n",
       "barcode    AACAACCTACATCGAAGC  AACAACCTACCACGAAGG  AACAACCTACTCGACTGC  \\\n",
       "ABCE1_1                     0                   7                   0   \n",
       "ABCE1_2                     0                   0                   0   \n",
       "ABHD17A_1                   0                   0                   0   \n",
       "ABHD17A_2                   0                   0                   0   \n",
       "ABHD17C_1                   0                   0                   0   \n",
       "...                       ...                 ...                 ...   \n",
       "ZP3_2                       0                   0                   0   \n",
       "ZRSR2_1                     0                   0                   0   \n",
       "ZRSR2_2                     0                   1                   0   \n",
       "ZWINT_1                     0                   1                   1   \n",
       "ZWINT_2                     0                   0                   0   \n",
       "\n",
       "barcode    AACAACCTAGCAGGAGAA  AACAACCTAGCCGAGTCT  AACAACCTAGCGAAGCTC  \\\n",
       "ABCE1_1                     0                   0                   3   \n",
       "ABCE1_2                     0                   0                   0   \n",
       "ABHD17A_1                   0                   0                   0   \n",
       "ABHD17A_2                   0                   0                   0   \n",
       "ABHD17C_1                   0                   0                   0   \n",
       "...                       ...                 ...                 ...   \n",
       "ZP3_2                       0                   0                   0   \n",
       "ZRSR2_1                     0                   0                   0   \n",
       "ZRSR2_2                     0                   0                   0   \n",
       "ZWINT_1                     0                   0                   3   \n",
       "ZWINT_2                     0                   0                   1   \n",
       "\n",
       "barcode    AACAACCTATAGAGCCAG  ...  TTGTCAACCTGTAACAGT  TTGTCAACCTTGATCGTA  \\\n",
       "ABCE1_1                     0  ...                   2                   2   \n",
       "ABCE1_2                     0  ...                   0                   0   \n",
       "ABHD17A_1                   0  ...                   2                   1   \n",
       "ABHD17A_2                   0  ...                   0                   0   \n",
       "ABHD17C_1                   0  ...                   0                   0   \n",
       "...                       ...  ...                 ...                 ...   \n",
       "ZP3_2                       0  ...                   0                   0   \n",
       "ZRSR2_1                     0  ...                   1                   1   \n",
       "ZRSR2_2                     0  ...                   0                   1   \n",
       "ZWINT_1                     2  ...                   1                   2   \n",
       "ZWINT_2                     0  ...                   0                   0   \n",
       "\n",
       "barcode    TTGTTAGAGACGCTAGTG  TTGTTAGAGATTCGAAGA  TTGTTAGAGCAACGATCG  \\\n",
       "ABCE1_1                     1                   3                   0   \n",
       "ABCE1_2                     0                   0                   0   \n",
       "ABHD17A_1                   2                   1                   0   \n",
       "ABHD17A_2                   0                   0                   0   \n",
       "ABHD17C_1                   0                   0                   0   \n",
       "...                       ...                 ...                 ...   \n",
       "ZP3_2                       0                   2                   0   \n",
       "ZRSR2_1                     1                   1                   0   \n",
       "ZRSR2_2                     0                   0                   0   \n",
       "ZWINT_1                     0                   3                   0   \n",
       "ZWINT_2                     0                   2                   0   \n",
       "\n",
       "barcode    TTGTTAGAGCCGCTATCC  TTGTTAGAGGTCCTAGTT  TTGTTAGAGTACTAGTAG  \\\n",
       "ABCE1_1                     0                   2                   0   \n",
       "ABCE1_2                     0                   0                   0   \n",
       "ABHD17A_1                   0                   0                   0   \n",
       "ABHD17A_2                   0                   0                   0   \n",
       "ABHD17C_1                   0                   0                   0   \n",
       "...                       ...                 ...                 ...   \n",
       "ZP3_2                       0                   1                   1   \n",
       "ZRSR2_1                     0                   0                   0   \n",
       "ZRSR2_2                     0                   0                   0   \n",
       "ZWINT_1                     0                   1                   1   \n",
       "ZWINT_2                     0                   0                   0   \n",
       "\n",
       "barcode    TTGTTAGAGTAGCGCAGC  TTGTTAGAGTGAACGTCA  \n",
       "ABCE1_1                    12                   3  \n",
       "ABCE1_2                     0                   0  \n",
       "ABHD17A_1                   4                   1  \n",
       "ABHD17A_2                   0                   0  \n",
       "ABHD17C_1                   0                   0  \n",
       "...                       ...                 ...  \n",
       "ZP3_2                       1                   0  \n",
       "ZRSR2_1                     1                   0  \n",
       "ZRSR2_2                     1                   0  \n",
       "ZWINT_1                     8                   1  \n",
       "ZWINT_2                     0                   0  \n",
       "\n",
       "[2342 rows x 17267 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "RNA_bygenes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "c0de4bd6-89da-45ea-a0a6-844eb4b9435b",
   "metadata": {},
   "outputs": [],
   "source": [
    "RNA_bygenes['genes'] = RNA_bygenes.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "723f0665-d677-40e3-842c-52e6f73cdf05",
   "metadata": {},
   "outputs": [],
   "source": [
    "RNA_bygenes['genes'] = RNA_bygenes.genes.apply(lambda x: x.split('_')[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "6393a264-227b-4b90-9bc3-ddd22b95eb11",
   "metadata": {},
   "outputs": [],
   "source": [
    "RNA_bygenes_grouped = RNA_bygenes.groupby('genes').mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "b9723d61-3b0b-4fdd-b72a-3ca90dc8cdc3",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/meb521/miniconda3/lib/python3.7/site-packages/ipykernel_launcher.py:1: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.\n",
      "  \"\"\"Entry point for launching an IPython kernel.\n"
     ]
    }
   ],
   "source": [
    "RNA_bygenes_grouped = AnnData(RNA_bygenes_grouped.T)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "3632a6be-14f3-47b5-929c-af674e73567c",
   "metadata": {},
   "outputs": [],
   "source": [
    "RNA_bygenes_grouped.obs.index = RNA_bygenes_grouped.obs.index + '-1'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "09f8f196-7780-4a07-a9c2-85951b6afc82",
   "metadata": {},
   "outputs": [],
   "source": [
    "RNA_bygenes_grouped.X = csr_matrix(RNA_bygenes_grouped.X)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "d33f06f6-c399-4b8b-a436-0bbfa7d6a104",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata = RNA_bygenes_grouped.copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "34a3a3c8-474a-443f-b416-5fa5c59636ee",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 17267 × 1201"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "8a65af17-f0ba-45e6-90c1-4148844538aa",
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.pp.filter_genes(adata, min_counts=1)\n",
    "sc.pp.filter_cells(adata, min_genes=30)\n",
    "sc.pp.calculate_qc_metrics(adata, percent_top=None, log1p=None, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "78bbc676-d1c1-47be-bb21-35ad626d2df0",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.obs['log10_genes'] = np.log10(adata.obs.n_genes_by_counts)\n",
    "adata.obs['log10_counts'] = np.log10(adata.obs.total_counts)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "fc847d79-56ae-4d31-91a7-247eb20e0ed1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 17237 × 1201\n",
       "    obs: 'n_genes', 'n_genes_by_counts', 'total_counts', 'log10_genes', 'log10_counts'\n",
       "    var: 'n_counts', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts'"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "id": "8410fdcb-cf05-4a35-be2b-3e9f8e47b3f9",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.write_h5ad('AML1026_2_mean.h5ad', compression='gzip')"
   ]
  }
 ],
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  "kernelspec": {
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