tutorial/demo2.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "## Demonstration of Bulk2Space on demo2 dataset"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "markdown",
   "source": [
    "### Import Bulk2Space"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "2f8064e5",
   "metadata": {},
   "outputs": [],
   "source": [
    "from bulk2space import Bulk2Space\n",
    "model = Bulk2Space()"
   ]
  },
  {
   "cell_type": "markdown",
   "source": [
    "### Decompose bulk-seq data into scRNA-seq data"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "markdown",
   "source": [
    "Train β-VAE model to generate scRNA-seq data"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "2600aa62",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading data......\n",
      "load data done!\n",
      "begin vae training...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Train Epoch: 19: 100%|█| 20/20 [00:02<00:00,  8.51it/s, loss=0.2070, min_lo\n",
      "generating: 100%|███████████████████| 999/999.0 [00:00<00:00, 27540.60it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "min loss = 0.20695747435092926\n",
      "vae training done!\n",
      "save trained vae in tutorial/data/example_data/demo2/predata/save_model/demo2_vae.pth.\n",
      "generating....\n",
      "generated done!\n",
      "saving to tutorial/data/example_data/demo2/predata/output/demo2_celltype_pred.csv and tutorial/data/example_data/demo2/predata/output/demo2_data_pred.csv.\n"
     ]
    }
   ],
   "source": [
    "generate_sc_meta, generate_sc_data = model.train_vae_and_generate(\n",
    "    input_bulk_path='tutorial/data/example_data/demo2/demo2_bulk.csv',\n",
    "    input_sc_data_path='tutorial/data/example_data/demo2/demo2_sc_data.csv',\n",
    "    input_sc_meta_path='tutorial/data/example_data/demo2/demo2_sc_meta.csv',\n",
    "    input_st_data_path='tutorial/data/example_data/demo2/demo2_st_data.csv',\n",
    "    input_st_meta_path='tutorial/data/example_data/demo2/demo2_st_meta.csv',\n",
    "    ratio_num=1,\n",
    "    top_marker_num=500,\n",
    "    gpu=0,\n",
    "    batch_size=512,\n",
    "    learning_rate=1e-4,\n",
    "    hidden_size=256,\n",
    "    epoch_num=20,\n",
    "    vae_save_dir='tutorial/data/example_data/demo2/predata/save_model',\n",
    "    vae_save_name='demo2_vae',\n",
    "    generate_save_dir='tutorial/data/example_data/demo2/predata/output',\n",
    "    generate_save_name='demo2')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "e4e20b25",
   "metadata": {},
   "outputs": [
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       "      Cell   Cell_type\n",
       "0      C_1  Inhibitory\n",
       "1      C_2   OD Mature\n",
       "2      C_3  Inhibitory\n",
       "3      C_4  Inhibitory\n",
       "4      C_5  Excitatory\n",
       "..     ...         ...\n",
       "994  C_995  Excitatory\n",
       "995  C_996  Excitatory\n",
       "996  C_997  Excitatory\n",
       "997  C_998  Excitatory\n",
       "998  C_999  Excitatory\n",
       "\n",
       "[999 rows x 2 columns]"
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     "execution_count": 3,
     "metadata": {},
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    "generate_sc_meta"
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  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "d043ba01",
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       "                    C_1       C_2       C_3       C_4       C_5       C_6  \\\n",
       "A730036I17Rik  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Sqrdl          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Pcdhb15        0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Irs4           0.229258  0.187985  0.204014  0.152463  0.260207  0.212885   \n",
       "Lmx1b          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "...                 ...       ...       ...       ...       ...       ...   \n",
       "Awat1          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
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       "\n",
       "                    C_7       C_8      C_9      C_10  ...     C_990     C_991  \\\n",
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       "Lmx1b          0.000000  0.000000  0.00000  0.000000  ...  0.000000  0.000000   \n",
       "...                 ...       ...      ...       ...  ...       ...       ...   \n",
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       "Snupn          0.000000  0.000000  0.00000  0.000000  ...  0.000000  0.000000   \n",
       "Abi3           0.000000  0.000000  0.00000  0.000000  ...  0.000000  0.000000   \n",
       "Ift88os        0.000000  0.000000  0.00000  0.000000  ...  0.000000  0.000000   \n",
       "Zc3hav1        0.000000  0.000000  0.00000  0.000000  ...  0.000000  0.000000   \n",
       "\n",
       "                  C_992     C_993     C_994     C_995     C_996     C_997  \\\n",
       "A730036I17Rik  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Sqrdl          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Pcdhb15        0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Irs4           0.248961  0.234014  0.227175  0.239612  0.235761  0.250142   \n",
       "Lmx1b          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "...                 ...       ...       ...       ...       ...       ...   \n",
       "Awat1          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Snupn          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Abi3           0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Ift88os        0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Zc3hav1        0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "\n",
       "                  C_998     C_999  \n",
       "A730036I17Rik  0.000000  0.000000  \n",
       "Sqrdl          0.000000  0.000000  \n",
       "Pcdhb15        0.000000  0.000000  \n",
       "Irs4           0.196212  0.181679  \n",
       "Lmx1b          0.000000  0.000000  \n",
       "...                 ...       ...  \n",
       "Awat1          0.000000  0.000000  \n",
       "Snupn          0.000000  0.000000  \n",
       "Abi3           0.000000  0.000000  \n",
       "Ift88os        0.000000  0.000000  \n",
       "Zc3hav1        0.000000  0.000000  \n",
       "\n",
       "[2910 rows x 999 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "generate_sc_data"
   ]
  },
  {
   "cell_type": "markdown",
   "source": [
    "Load trained β-VAE model to generate scRNA-seq data"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "1a148324",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading data......\n",
      "load data done!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      "generating:   0%|                                | 0/999.0 [00:00<?, ?it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading model from tutorial/data/example_data/demo2/predata/save_model/demo2_vae.pth\n",
      "generating....\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "generating: 100%|███████████████████| 999/999.0 [00:00<00:00, 27253.81it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "generated done!\n",
      "saving to tutorial/data/example_data/demo2/predata/output/demo2_new_celltype_pred.csv and tutorial/data/example_data/demo2/predata/output/demo2_new_data_pred.csv.\n",
      "generating done!\n"
     ]
    }
   ],
   "source": [
    "generate_sc_meta, generate_sc_data = model.load_vae_and_generate(\n",
    "    input_bulk_path='tutorial/data/example_data/demo2/demo2_bulk.csv',\n",
    "    input_sc_data_path='tutorial/data/example_data/demo2/demo2_sc_data.csv',\n",
    "    input_sc_meta_path='tutorial/data/example_data/demo2/demo2_sc_meta.csv',\n",
    "    input_st_data_path='tutorial/data/example_data/demo2/demo2_st_data.csv',\n",
    "    input_st_meta_path='tutorial/data/example_data/demo2/demo2_st_meta.csv',\n",
    "    vae_load_dir='tutorial/data/example_data/demo2/predata/save_model/demo2_vae.pth',\n",
    "    generate_save_dir='tutorial/data/example_data/demo2/predata/output', \n",
    "    generate_save_name='demo2_new',\n",
    "    ratio_num=1,\n",
    "    top_marker_num=500)"
   ]
  },
  {
   "cell_type": "markdown",
   "source": [
    "### Map image-based spatial transcriptomics data into spatially resolved single-cell transcriptomics data"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "01e84e5a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "start to process image-based st data...\n",
      "saving to output/meta_map.csv and output/data_map.csv\n"
     ]
    }
   ],
   "source": [
    "df_meta, df_data = model.spatial_mapping(\n",
    "    generate_sc_meta,\n",
    "    generate_sc_data,\n",
    "    input_st_data_path='tutorial/data/example_data/demo2/demo2_st_data.csv',\n",
    "    input_st_meta_path='tutorial/data/example_data/demo2/demo2_st_meta.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "40fb4696",
   "metadata": {},
   "outputs": [
    {
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       "    <tr>\n",
       "      <th>499</th>\n",
       "      <td>ST_500</td>\n",
       "      <td>Inhibitory</td>\n",
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       "      <td>1763.950629</td>\n",
       "      <td>-3292.651727</td>\n",
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       "<p>500 rows × 5 columns</p>\n",
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       "       Cell Cell_type_x  Cell_type_y       xcoord       ycoord\n",
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       "1      ST_2   OD Mature   Inhibitory  1033.948518 -3919.292990\n",
       "2      ST_3  Inhibitory   Inhibitory   633.561019 -2745.446441\n",
       "3      ST_4  Inhibitory   Inhibitory   899.133783 -3795.596788\n",
       "4      ST_5  Inhibitory    Ambiguous  2006.857092 -3715.491887\n",
       "..      ...         ...          ...          ...          ...\n",
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       "496  ST_497  Inhibitory    Ambiguous   568.879625 -3866.576725\n",
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       "498  ST_499  Inhibitory  Endothelial  2032.940725 -2579.343161\n",
       "499  ST_500  Inhibitory    Microglia  1763.950629 -3292.651727\n",
       "\n",
       "[500 rows x 5 columns]"
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     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_meta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "ce2b3b1a",
   "metadata": {},
   "outputs": [
    {
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       "      <td>0.26738</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ift88os</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Zc3hav1</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2910 rows × 500 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   ST_1      ST_2      ST_3     ST_4      ST_5      ST_6  \\\n",
       "A730036I17Rik  0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "Sqrdl          0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "Pcdhb15        0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "Irs4           0.201062  0.286538  0.211379  0.26738  0.203618  0.189571   \n",
       "Lmx1b          0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "...                 ...       ...       ...      ...       ...       ...   \n",
       "Awat1          0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "Snupn          0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "Abi3           0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "Ift88os        0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "Zc3hav1        0.000000  0.000000  0.000000  0.00000  0.000000  0.000000   \n",
       "\n",
       "                   ST_7      ST_8      ST_9     ST_10  ...    ST_491  \\\n",
       "A730036I17Rik  0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "Sqrdl          0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "Pcdhb15        0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "Irs4           0.242153  0.187009  0.259919  0.188122  ...  0.245203   \n",
       "Lmx1b          0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "...                 ...       ...       ...       ...  ...       ...   \n",
       "Awat1          0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "Snupn          0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "Abi3           0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "Ift88os        0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "Zc3hav1        0.000000  0.000000  0.000000  0.000000  ...  0.000000   \n",
       "\n",
       "                 ST_492    ST_493    ST_494    ST_495    ST_496    ST_497  \\\n",
       "A730036I17Rik  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Sqrdl          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Pcdhb15        0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Irs4           0.210806  0.218806  0.281182  0.203533  0.190263  0.191078   \n",
       "Lmx1b          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "...                 ...       ...       ...       ...       ...       ...   \n",
       "Awat1          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Snupn          0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Abi3           0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Ift88os        0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "Zc3hav1        0.000000  0.000000  0.000000  0.000000  0.000000  0.000000   \n",
       "\n",
       "                 ST_498    ST_499    ST_500  \n",
       "A730036I17Rik  0.000000  0.000000  0.000000  \n",
       "Sqrdl          0.000000  0.000000  0.000000  \n",
       "Pcdhb15        0.000000  0.000000  0.000000  \n",
       "Irs4           0.204066  0.186952  0.186572  \n",
       "Lmx1b          0.000000  0.000000  0.000000  \n",
       "...                 ...       ...       ...  \n",
       "Awat1          0.000000  0.000000  0.000000  \n",
       "Snupn          0.000000  0.000000  0.000000  \n",
       "Abi3           0.000000  0.000000  0.000000  \n",
       "Ift88os        0.000000  0.000000  0.000000  \n",
       "Zc3hav1        0.000000  0.000000  0.000000  \n",
       "\n",
       "[2910 rows x 500 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d01cc354",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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