tutorial.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tutorial"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Prepare Inputs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import warnings\n",
    "warnings.filterwarnings(\"ignore\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### BCRs input file, BCR_original_emb file, and rna input file\n",
    "1. Ensure that each file includes an index column labeled \"barcode\". This column serves as a unique identifier for each cell.\n",
    "2. Verify that the cells are aligned in the same order across all three files.\n",
    "3. The BCR file must include the following columns: \"cdr1\", \"cdr2\", \"fwr2\", \"cdr3\", \"fwr3\", and \"fwr4\"."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "bcr = pd.read_csv(\"exampledata/example_bcr.csv\", index_col=\"barcode\")\n",
    "rna = pd.read_csv(\"exampledata/example_rna.csv\", index_col=\"barcode\")\n",
    "assert(bcr.index.tolist() == rna.index.tolist())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>contig_id</th>\n",
       "      <th>is_cell</th>\n",
       "      <th>high_confidence</th>\n",
       "      <th>length</th>\n",
       "      <th>chain</th>\n",
       "      <th>v_gene</th>\n",
       "      <th>d_gene</th>\n",
       "      <th>j_gene</th>\n",
       "      <th>c_gene</th>\n",
       "      <th>full_length</th>\n",
       "      <th>...</th>\n",
       "      <th>umis</th>\n",
       "      <th>raw_clonotype_id</th>\n",
       "      <th>raw_consensus_id</th>\n",
       "      <th>exact_subclonotype_id</th>\n",
       "      <th>sample</th>\n",
       "      <th>label</th>\n",
       "      <th>whole_seq</th>\n",
       "      <th>new_whole_seq</th>\n",
       "      <th>v_identity</th>\n",
       "      <th>SHM</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>barcode</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>AAACCTGCAATAGCAA-1_06</th>\n",
       "      <td>AAACCTGCAATAGCAA-1_contig_1_06</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>619</td>\n",
       "      <td>IGH</td>\n",
       "      <td>IGHV2-5</td>\n",
       "      <td>NaN</td>\n",
       "      <td>IGHJ4</td>\n",
       "      <td>IGHG1</td>\n",
       "      <td>True</td>\n",
       "      <td>...</td>\n",
       "      <td>5</td>\n",
       "      <td>clonotype455</td>\n",
       "      <td>clonotype455_consensus_1</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>spikepositive</td>\n",
       "      <td>QITLKESGPTLVKPTQTLTLTCTFSGFSLTSGMGVGWIRQPPGKAL...</td>\n",
       "      <td>06:QITLKESGPTLVKPTQTLTLTCTFSGFSLTSGMGVGWIRQPPG...</td>\n",
       "      <td>0.03754</td>\n",
       "      <td>0.061453</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCACAACTGT-1_06</th>\n",
       "      <td>AAACCTGCACAACTGT-1_contig_2_06</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>537</td>\n",
       "      <td>IGH</td>\n",
       "      <td>IGHV1-24</td>\n",
       "      <td>NaN</td>\n",
       "      <td>IGHJ4</td>\n",
       "      <td>IGHM</td>\n",
       "      <td>True</td>\n",
       "      <td>...</td>\n",
       "      <td>52</td>\n",
       "      <td>clonotype278</td>\n",
       "      <td>clonotype278_consensus_1</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>spikepositive</td>\n",
       "      <td>QVQLVQSGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLE...</td>\n",
       "      <td>06:QVQLVQSGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGK...</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.008596</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGCCTGTG-1_06</th>\n",
       "      <td>AAACCTGCAGCCTGTG-1_contig_1_06</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>656</td>\n",
       "      <td>IGH</td>\n",
       "      <td>IGHV4-59</td>\n",
       "      <td>IGHD3-22</td>\n",
       "      <td>IGHJ4</td>\n",
       "      <td>IGHG1</td>\n",
       "      <td>True</td>\n",
       "      <td>...</td>\n",
       "      <td>8</td>\n",
       "      <td>clonotype1394</td>\n",
       "      <td>clonotype1394_consensus_1</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>spikepositive</td>\n",
       "      <td>QVQLQESGPGLVKPSETLSLICTVSGGSISSYYWSWIRQPAGKGLE...</td>\n",
       "      <td>06:QVQLQESGPGLVKPSETLSLICTVSGGSISSYYWSWIRQPAGK...</td>\n",
       "      <td>0.02397</td>\n",
       "      <td>0.066489</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGTCAGCC-1_06</th>\n",
       "      <td>AAACCTGCAGTCAGCC-1_contig_2_06</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>670</td>\n",
       "      <td>IGH</td>\n",
       "      <td>IGHV1-2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>IGHJ5</td>\n",
       "      <td>IGHG1</td>\n",
       "      <td>True</td>\n",
       "      <td>...</td>\n",
       "      <td>8</td>\n",
       "      <td>clonotype969</td>\n",
       "      <td>clonotype969_consensus_1</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>spikepositive</td>\n",
       "      <td>QVQLVQSGAEVKNIGVSVKVSCKASGYTFTDYYIHWVRQAPGQGLE...</td>\n",
       "      <td>06:QVQLVQSGAEVKNIGVSVKVSCKASGYTFTDYYIHWVRQAPGQ...</td>\n",
       "      <td>0.06081</td>\n",
       "      <td>0.095368</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTTCCTCCA-1_06</th>\n",
       "      <td>AAACCTGGTTCCTCCA-1_contig_2_06</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>692</td>\n",
       "      <td>IGH</td>\n",
       "      <td>IGHV1-18</td>\n",
       "      <td>IGHD3-22</td>\n",
       "      <td>IGHJ4</td>\n",
       "      <td>IGHG1</td>\n",
       "      <td>True</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>clonotype1466</td>\n",
       "      <td>clonotype1466_consensus_1</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>spikepositive</td>\n",
       "      <td>QVQLVQSGDEVKKPGASVKVSCEASGYTFISYGIAWVRQAPGQGLE...</td>\n",
       "      <td>06:QVQLVQSGDEVKKPGASVKVSCEASGYTFISYGIAWVRQAPGQ...</td>\n",
       "      <td>0.11576</td>\n",
       "      <td>0.139594</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 36 columns</p>\n",
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      ],
      "text/plain": [
       "                                            contig_id  is_cell  \\\n",
       "barcode                                                          \n",
       "AAACCTGCAATAGCAA-1_06  AAACCTGCAATAGCAA-1_contig_1_06     True   \n",
       "AAACCTGCACAACTGT-1_06  AAACCTGCACAACTGT-1_contig_2_06     True   \n",
       "AAACCTGCAGCCTGTG-1_06  AAACCTGCAGCCTGTG-1_contig_1_06     True   \n",
       "AAACCTGCAGTCAGCC-1_06  AAACCTGCAGTCAGCC-1_contig_2_06     True   \n",
       "AAACCTGGTTCCTCCA-1_06  AAACCTGGTTCCTCCA-1_contig_2_06     True   \n",
       "\n",
       "                       high_confidence  length chain    v_gene    d_gene  \\\n",
       "barcode                                                                    \n",
       "AAACCTGCAATAGCAA-1_06             True     619   IGH   IGHV2-5       NaN   \n",
       "AAACCTGCACAACTGT-1_06             True     537   IGH  IGHV1-24       NaN   \n",
       "AAACCTGCAGCCTGTG-1_06             True     656   IGH  IGHV4-59  IGHD3-22   \n",
       "AAACCTGCAGTCAGCC-1_06             True     670   IGH   IGHV1-2       NaN   \n",
       "AAACCTGGTTCCTCCA-1_06             True     692   IGH  IGHV1-18  IGHD3-22   \n",
       "\n",
       "                      j_gene c_gene  full_length  ...  umis raw_clonotype_id  \\\n",
       "barcode                                           ...                          \n",
       "AAACCTGCAATAGCAA-1_06  IGHJ4  IGHG1         True  ...     5     clonotype455   \n",
       "AAACCTGCACAACTGT-1_06  IGHJ4   IGHM         True  ...    52     clonotype278   \n",
       "AAACCTGCAGCCTGTG-1_06  IGHJ4  IGHG1         True  ...     8    clonotype1394   \n",
       "AAACCTGCAGTCAGCC-1_06  IGHJ5  IGHG1         True  ...     8     clonotype969   \n",
       "AAACCTGGTTCCTCCA-1_06  IGHJ4  IGHG1         True  ...    21    clonotype1466   \n",
       "\n",
       "                                raw_consensus_id exact_subclonotype_id sample  \\\n",
       "barcode                                                                         \n",
       "AAACCTGCAATAGCAA-1_06   clonotype455_consensus_1                     1      6   \n",
       "AAACCTGCACAACTGT-1_06   clonotype278_consensus_1                     1      6   \n",
       "AAACCTGCAGCCTGTG-1_06  clonotype1394_consensus_1                     1      6   \n",
       "AAACCTGCAGTCAGCC-1_06   clonotype969_consensus_1                     1      6   \n",
       "AAACCTGGTTCCTCCA-1_06  clonotype1466_consensus_1                     1      6   \n",
       "\n",
       "                               label  \\\n",
       "barcode                                \n",
       "AAACCTGCAATAGCAA-1_06  spikepositive   \n",
       "AAACCTGCACAACTGT-1_06  spikepositive   \n",
       "AAACCTGCAGCCTGTG-1_06  spikepositive   \n",
       "AAACCTGCAGTCAGCC-1_06  spikepositive   \n",
       "AAACCTGGTTCCTCCA-1_06  spikepositive   \n",
       "\n",
       "                                                               whole_seq  \\\n",
       "barcode                                                                    \n",
       "AAACCTGCAATAGCAA-1_06  QITLKESGPTLVKPTQTLTLTCTFSGFSLTSGMGVGWIRQPPGKAL...   \n",
       "AAACCTGCACAACTGT-1_06  QVQLVQSGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLE...   \n",
       "AAACCTGCAGCCTGTG-1_06  QVQLQESGPGLVKPSETLSLICTVSGGSISSYYWSWIRQPAGKGLE...   \n",
       "AAACCTGCAGTCAGCC-1_06  QVQLVQSGAEVKNIGVSVKVSCKASGYTFTDYYIHWVRQAPGQGLE...   \n",
       "AAACCTGGTTCCTCCA-1_06  QVQLVQSGDEVKKPGASVKVSCEASGYTFISYGIAWVRQAPGQGLE...   \n",
       "\n",
       "                                                           new_whole_seq  \\\n",
       "barcode                                                                    \n",
       "AAACCTGCAATAGCAA-1_06  06:QITLKESGPTLVKPTQTLTLTCTFSGFSLTSGMGVGWIRQPPG...   \n",
       "AAACCTGCACAACTGT-1_06  06:QVQLVQSGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGK...   \n",
       "AAACCTGCAGCCTGTG-1_06  06:QVQLQESGPGLVKPSETLSLICTVSGGSISSYYWSWIRQPAGK...   \n",
       "AAACCTGCAGTCAGCC-1_06  06:QVQLVQSGAEVKNIGVSVKVSCKASGYTFTDYYIHWVRQAPGQ...   \n",
       "AAACCTGGTTCCTCCA-1_06  06:QVQLVQSGDEVKKPGASVKVSCEASGYTFISYGIAWVRQAPGQ...   \n",
       "\n",
       "                      v_identity       SHM  \n",
       "barcode                                     \n",
       "AAACCTGCAATAGCAA-1_06    0.03754  0.061453  \n",
       "AAACCTGCACAACTGT-1_06    0.00000  0.008596  \n",
       "AAACCTGCAGCCTGTG-1_06    0.02397  0.066489  \n",
       "AAACCTGCAGTCAGCC-1_06    0.06081  0.095368  \n",
       "AAACCTGGTTCCTCCA-1_06    0.11576  0.139594  \n",
       "\n",
       "[5 rows x 36 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bcr.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>IGJ</th>\n",
       "      <th>IGLL5</th>\n",
       "      <th>RP11.685N3.1</th>\n",
       "      <th>RP11.731F5.2</th>\n",
       "      <th>CH17.132F21.1</th>\n",
       "      <th>HIST1H4C</th>\n",
       "      <th>UBE2C</th>\n",
       "      <th>DERL3</th>\n",
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       "      <th>BFSP2.AS1</th>\n",
       "      <th>PIK3CA</th>\n",
       "      <th>TARSL2</th>\n",
       "      <th>DIS3</th>\n",
       "      <th>CTD.2256P15.2</th>\n",
       "      <th>ZNF283</th>\n",
       "      <th>FAHD2B</th>\n",
       "      <th>RP11.485G4.2</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>barcode</th>\n",
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       "      <th>AAACCTGCAATAGCAA-1_06</th>\n",
       "      <td>0.345539</td>\n",
       "      <td>0.411600</td>\n",
       "      <td>-0.086132</td>\n",
       "      <td>-0.151236</td>\n",
       "      <td>0.034590</td>\n",
       "      <td>0.737681</td>\n",
       "      <td>0.000468</td>\n",
       "      <td>0.122183</td>\n",
       "      <td>1.349319</td>\n",
       "      <td>0.002903</td>\n",
       "      <td>...</td>\n",
       "      <td>0.771746</td>\n",
       "      <td>-0.000238</td>\n",
       "      <td>0.000177</td>\n",
       "      <td>0.016492</td>\n",
       "      <td>0.660869</td>\n",
       "      <td>-0.059796</td>\n",
       "      <td>0.012625</td>\n",
       "      <td>0.007151</td>\n",
       "      <td>0.014972</td>\n",
       "      <td>0.026571</td>\n",
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       "      <th>AAACCTGCACAACTGT-1_06</th>\n",
       "      <td>0.117444</td>\n",
       "      <td>0.985152</td>\n",
       "      <td>-0.210269</td>\n",
       "      <td>-0.231358</td>\n",
       "      <td>-0.074831</td>\n",
       "      <td>1.304759</td>\n",
       "      <td>-0.003087</td>\n",
       "      <td>0.564784</td>\n",
       "      <td>0.796385</td>\n",
       "      <td>0.000614</td>\n",
       "      <td>...</td>\n",
       "      <td>0.126555</td>\n",
       "      <td>-0.057113</td>\n",
       "      <td>0.000036</td>\n",
       "      <td>0.127062</td>\n",
       "      <td>0.248703</td>\n",
       "      <td>0.093876</td>\n",
       "      <td>0.005728</td>\n",
       "      <td>0.025548</td>\n",
       "      <td>0.009291</td>\n",
       "      <td>-0.002509</td>\n",
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       "    <tr>\n",
       "      <th>AAACCTGCAGCCTGTG-1_06</th>\n",
       "      <td>0.118185</td>\n",
       "      <td>0.304202</td>\n",
       "      <td>1.553921</td>\n",
       "      <td>-0.071504</td>\n",
       "      <td>-0.152440</td>\n",
       "      <td>1.007265</td>\n",
       "      <td>-0.005297</td>\n",
       "      <td>0.122008</td>\n",
       "      <td>1.350721</td>\n",
       "      <td>0.001795</td>\n",
       "      <td>...</td>\n",
       "      <td>0.008371</td>\n",
       "      <td>-0.001826</td>\n",
       "      <td>0.000120</td>\n",
       "      <td>-0.070642</td>\n",
       "      <td>-0.085906</td>\n",
       "      <td>0.005892</td>\n",
       "      <td>-0.018601</td>\n",
       "      <td>0.030213</td>\n",
       "      <td>-0.042815</td>\n",
       "      <td>-0.001975</td>\n",
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       "    <tr>\n",
       "      <th>AAACCTGCAGTCAGCC-1_06</th>\n",
       "      <td>0.123230</td>\n",
       "      <td>1.773176</td>\n",
       "      <td>-0.150341</td>\n",
       "      <td>-0.035437</td>\n",
       "      <td>0.003177</td>\n",
       "      <td>0.666422</td>\n",
       "      <td>0.046367</td>\n",
       "      <td>0.030498</td>\n",
       "      <td>1.141658</td>\n",
       "      <td>0.000546</td>\n",
       "      <td>...</td>\n",
       "      <td>0.069885</td>\n",
       "      <td>-0.079806</td>\n",
       "      <td>0.000041</td>\n",
       "      <td>0.015928</td>\n",
       "      <td>0.099969</td>\n",
       "      <td>0.084648</td>\n",
       "      <td>0.014874</td>\n",
       "      <td>-0.017749</td>\n",
       "      <td>0.041447</td>\n",
       "      <td>0.007477</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTTCCTCCA-1_06</th>\n",
       "      <td>0.162600</td>\n",
       "      <td>0.300888</td>\n",
       "      <td>-0.164492</td>\n",
       "      <td>0.755047</td>\n",
       "      <td>-0.039643</td>\n",
       "      <td>0.022945</td>\n",
       "      <td>0.017033</td>\n",
       "      <td>0.154383</td>\n",
       "      <td>0.842697</td>\n",
       "      <td>0.007529</td>\n",
       "      <td>...</td>\n",
       "      <td>0.025873</td>\n",
       "      <td>0.010463</td>\n",
       "      <td>-0.009411</td>\n",
       "      <td>0.573100</td>\n",
       "      <td>-0.028001</td>\n",
       "      <td>0.097279</td>\n",
       "      <td>0.011172</td>\n",
       "      <td>0.013083</td>\n",
       "      <td>0.161455</td>\n",
       "      <td>-0.006934</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 5000 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                            IGJ     IGLL5  RP11.685N3.1  RP11.731F5.2  \\\n",
       "barcode                                                                 \n",
       "AAACCTGCAATAGCAA-1_06  0.345539  0.411600     -0.086132     -0.151236   \n",
       "AAACCTGCACAACTGT-1_06  0.117444  0.985152     -0.210269     -0.231358   \n",
       "AAACCTGCAGCCTGTG-1_06  0.118185  0.304202      1.553921     -0.071504   \n",
       "AAACCTGCAGTCAGCC-1_06  0.123230  1.773176     -0.150341     -0.035437   \n",
       "AAACCTGGTTCCTCCA-1_06  0.162600  0.300888     -0.164492      0.755047   \n",
       "\n",
       "                       CH17.132F21.1  HIST1H4C     UBE2C     DERL3    TUBA1B  \\\n",
       "barcode                                                                        \n",
       "AAACCTGCAATAGCAA-1_06       0.034590  0.737681  0.000468  0.122183  1.349319   \n",
       "AAACCTGCACAACTGT-1_06      -0.074831  1.304759 -0.003087  0.564784  0.796385   \n",
       "AAACCTGCAGCCTGTG-1_06      -0.152440  1.007265 -0.005297  0.122008  1.350721   \n",
       "AAACCTGCAGTCAGCC-1_06       0.003177  0.666422  0.046367  0.030498  1.141658   \n",
       "AAACCTGGTTCCTCCA-1_06      -0.039643  0.022945  0.017033  0.154383  0.842697   \n",
       "\n",
       "                          MKI67  ...      AZI2     HHLA3  BFSP2.AS1    PIK3CA  \\\n",
       "barcode                          ...                                            \n",
       "AAACCTGCAATAGCAA-1_06  0.002903  ...  0.771746 -0.000238   0.000177  0.016492   \n",
       "AAACCTGCACAACTGT-1_06  0.000614  ...  0.126555 -0.057113   0.000036  0.127062   \n",
       "AAACCTGCAGCCTGTG-1_06  0.001795  ...  0.008371 -0.001826   0.000120 -0.070642   \n",
       "AAACCTGCAGTCAGCC-1_06  0.000546  ...  0.069885 -0.079806   0.000041  0.015928   \n",
       "AAACCTGGTTCCTCCA-1_06  0.007529  ...  0.025873  0.010463  -0.009411  0.573100   \n",
       "\n",
       "                         TARSL2      DIS3  CTD.2256P15.2    ZNF283    FAHD2B  \\\n",
       "barcode                                                                        \n",
       "AAACCTGCAATAGCAA-1_06  0.660869 -0.059796       0.012625  0.007151  0.014972   \n",
       "AAACCTGCACAACTGT-1_06  0.248703  0.093876       0.005728  0.025548  0.009291   \n",
       "AAACCTGCAGCCTGTG-1_06 -0.085906  0.005892      -0.018601  0.030213 -0.042815   \n",
       "AAACCTGCAGTCAGCC-1_06  0.099969  0.084648       0.014874 -0.017749  0.041447   \n",
       "AAACCTGGTTCCTCCA-1_06 -0.028001  0.097279       0.011172  0.013083  0.161455   \n",
       "\n",
       "                       RP11.485G4.2  \n",
       "barcode                              \n",
       "AAACCTGCAATAGCAA-1_06      0.026571  \n",
       "AAACCTGCACAACTGT-1_06     -0.002509  \n",
       "AAACCTGCAGCCTGTG-1_06     -0.001975  \n",
       "AAACCTGCAGTCAGCC-1_06      0.007477  \n",
       "AAACCTGGTTCCTCCA-1_06     -0.006934  \n",
       "\n",
       "[5 rows x 5000 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rna.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Genreate original BCR embeddings\n",
    "\n",
    "First, we download the pre-trained BCR encoder\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Fetching 8 files: 100%|██████████| 8/8 [00:05<00:00,  1.48it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Download Finished. Path /mnt/d/CoMBCR/CoMBCR/BCRencoder\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    }
   ],
   "source": [
    "from CoMBCR.utils import download_BCRencoder\n",
    "\n",
    "download_BCRencoder()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Please clone or download the \"runberta.py\" in this github. This file is used to measure the original distances between BCRs. We recommend using our default pre-trained encoder, though any encoder can be used to encode BCRs."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we directly used the original BCR embeddings under the exampledata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "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",
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       "    }\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>0</th>\n",
       "      <th>1</th>\n",
       "      <th>2</th>\n",
       "      <th>3</th>\n",
       "      <th>4</th>\n",
       "      <th>5</th>\n",
       "      <th>6</th>\n",
       "      <th>7</th>\n",
       "      <th>8</th>\n",
       "      <th>9</th>\n",
       "      <th>...</th>\n",
       "      <th>1014</th>\n",
       "      <th>1015</th>\n",
       "      <th>1016</th>\n",
       "      <th>1017</th>\n",
       "      <th>1018</th>\n",
       "      <th>1019</th>\n",
       "      <th>1020</th>\n",
       "      <th>1021</th>\n",
       "      <th>1022</th>\n",
       "      <th>1023</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>barcode</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>AAACCTGCAATAGCAA-1_06</th>\n",
       "      <td>-0.324237</td>\n",
       "      <td>-0.228240</td>\n",
       "      <td>-0.241070</td>\n",
       "      <td>0.951063</td>\n",
       "      <td>-0.688552</td>\n",
       "      <td>-0.024392</td>\n",
       "      <td>-0.455126</td>\n",
       "      <td>-0.142796</td>\n",
       "      <td>0.071060</td>\n",
       "      <td>0.872651</td>\n",
       "      <td>...</td>\n",
       "      <td>0.433799</td>\n",
       "      <td>-0.089641</td>\n",
       "      <td>0.199088</td>\n",
       "      <td>-0.619232</td>\n",
       "      <td>0.433234</td>\n",
       "      <td>-0.507768</td>\n",
       "      <td>0.094147</td>\n",
       "      <td>0.622088</td>\n",
       "      <td>-0.438514</td>\n",
       "      <td>-0.548302</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCACAACTGT-1_06</th>\n",
       "      <td>-0.836004</td>\n",
       "      <td>-0.281383</td>\n",
       "      <td>-1.062309</td>\n",
       "      <td>0.253088</td>\n",
       "      <td>-0.613961</td>\n",
       "      <td>0.173742</td>\n",
       "      <td>-0.924163</td>\n",
       "      <td>0.295760</td>\n",
       "      <td>0.215318</td>\n",
       "      <td>0.514034</td>\n",
       "      <td>...</td>\n",
       "      <td>0.113509</td>\n",
       "      <td>0.117395</td>\n",
       "      <td>-0.115959</td>\n",
       "      <td>-0.211876</td>\n",
       "      <td>0.793687</td>\n",
       "      <td>-0.666870</td>\n",
       "      <td>-0.068236</td>\n",
       "      <td>0.275671</td>\n",
       "      <td>0.094568</td>\n",
       "      <td>-0.396323</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGCCTGTG-1_06</th>\n",
       "      <td>-0.388252</td>\n",
       "      <td>-0.081444</td>\n",
       "      <td>-0.394865</td>\n",
       "      <td>1.480731</td>\n",
       "      <td>-0.288159</td>\n",
       "      <td>-0.132324</td>\n",
       "      <td>-0.263037</td>\n",
       "      <td>-0.209172</td>\n",
       "      <td>0.423102</td>\n",
       "      <td>0.569923</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.231537</td>\n",
       "      <td>-0.353619</td>\n",
       "      <td>0.118815</td>\n",
       "      <td>-1.144104</td>\n",
       "      <td>0.398278</td>\n",
       "      <td>0.067934</td>\n",
       "      <td>-0.181059</td>\n",
       "      <td>0.760884</td>\n",
       "      <td>-0.498049</td>\n",
       "      <td>-0.671089</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGTCAGCC-1_06</th>\n",
       "      <td>-0.912942</td>\n",
       "      <td>0.000863</td>\n",
       "      <td>0.077432</td>\n",
       "      <td>0.949241</td>\n",
       "      <td>0.020408</td>\n",
       "      <td>0.136745</td>\n",
       "      <td>-0.283928</td>\n",
       "      <td>-0.212797</td>\n",
       "      <td>0.105468</td>\n",
       "      <td>0.711840</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.587940</td>\n",
       "      <td>0.107624</td>\n",
       "      <td>-0.320966</td>\n",
       "      <td>-1.219826</td>\n",
       "      <td>0.783442</td>\n",
       "      <td>0.099214</td>\n",
       "      <td>0.109777</td>\n",
       "      <td>0.096048</td>\n",
       "      <td>-0.420305</td>\n",
       "      <td>-1.142159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTTCCTCCA-1_06</th>\n",
       "      <td>-0.079208</td>\n",
       "      <td>-0.455230</td>\n",
       "      <td>-0.978580</td>\n",
       "      <td>1.132275</td>\n",
       "      <td>-0.574163</td>\n",
       "      <td>0.258197</td>\n",
       "      <td>-0.157592</td>\n",
       "      <td>-0.350995</td>\n",
       "      <td>0.127573</td>\n",
       "      <td>0.343525</td>\n",
       "      <td>...</td>\n",
       "      <td>0.351599</td>\n",
       "      <td>-0.057017</td>\n",
       "      <td>0.099804</td>\n",
       "      <td>-1.488126</td>\n",
       "      <td>0.658145</td>\n",
       "      <td>0.039580</td>\n",
       "      <td>-0.006186</td>\n",
       "      <td>-0.196100</td>\n",
       "      <td>-0.564170</td>\n",
       "      <td>-0.376476</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 1024 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                              0         1         2         3         4  \\\n",
       "barcode                                                                   \n",
       "AAACCTGCAATAGCAA-1_06 -0.324237 -0.228240 -0.241070  0.951063 -0.688552   \n",
       "AAACCTGCACAACTGT-1_06 -0.836004 -0.281383 -1.062309  0.253088 -0.613961   \n",
       "AAACCTGCAGCCTGTG-1_06 -0.388252 -0.081444 -0.394865  1.480731 -0.288159   \n",
       "AAACCTGCAGTCAGCC-1_06 -0.912942  0.000863  0.077432  0.949241  0.020408   \n",
       "AAACCTGGTTCCTCCA-1_06 -0.079208 -0.455230 -0.978580  1.132275 -0.574163   \n",
       "\n",
       "                              5         6         7         8         9  ...  \\\n",
       "barcode                                                                  ...   \n",
       "AAACCTGCAATAGCAA-1_06 -0.024392 -0.455126 -0.142796  0.071060  0.872651  ...   \n",
       "AAACCTGCACAACTGT-1_06  0.173742 -0.924163  0.295760  0.215318  0.514034  ...   \n",
       "AAACCTGCAGCCTGTG-1_06 -0.132324 -0.263037 -0.209172  0.423102  0.569923  ...   \n",
       "AAACCTGCAGTCAGCC-1_06  0.136745 -0.283928 -0.212797  0.105468  0.711840  ...   \n",
       "AAACCTGGTTCCTCCA-1_06  0.258197 -0.157592 -0.350995  0.127573  0.343525  ...   \n",
       "\n",
       "                           1014      1015      1016      1017      1018  \\\n",
       "barcode                                                                   \n",
       "AAACCTGCAATAGCAA-1_06  0.433799 -0.089641  0.199088 -0.619232  0.433234   \n",
       "AAACCTGCACAACTGT-1_06  0.113509  0.117395 -0.115959 -0.211876  0.793687   \n",
       "AAACCTGCAGCCTGTG-1_06 -0.231537 -0.353619  0.118815 -1.144104  0.398278   \n",
       "AAACCTGCAGTCAGCC-1_06 -0.587940  0.107624 -0.320966 -1.219826  0.783442   \n",
       "AAACCTGGTTCCTCCA-1_06  0.351599 -0.057017  0.099804 -1.488126  0.658145   \n",
       "\n",
       "                           1019      1020      1021      1022      1023  \n",
       "barcode                                                                  \n",
       "AAACCTGCAATAGCAA-1_06 -0.507768  0.094147  0.622088 -0.438514 -0.548302  \n",
       "AAACCTGCACAACTGT-1_06 -0.666870 -0.068236  0.275671  0.094568 -0.396323  \n",
       "AAACCTGCAGCCTGTG-1_06  0.067934 -0.181059  0.760884 -0.498049 -0.671089  \n",
       "AAACCTGCAGTCAGCC-1_06  0.099214  0.109777  0.096048 -0.420305 -1.142159  \n",
       "AAACCTGGTTCCTCCA-1_06  0.039580 -0.006186 -0.196100 -0.564170 -0.376476  \n",
       "\n",
       "[5 rows x 1024 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bcrori = pd.read_csv(\"exampledata/example_bcrori.csv\", index_col=\"barcode\")\n",
    "bcrori.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "assert(bcr.index.tolist() == bcrori.index.tolist())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run CoMBCR"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## steps\n",
    "CoMBCR contains the parameters as follows:\n",
    "1. bcrpath: (Required) The path to the BCR sequences file.\n",
    "2. rnapath:  (Required) The path to the gene expression file.\n",
    "3. bcroriginal: (Required) The path to bcr original embedding file.\n",
    "4. outdir:  (Required) The directory where the best checkpoint file and the output embeddings will be stored.\n",
    "5. checkpoint: default is \"best_network.pth\". This parameter specifies the name of the file where the best model checkpoint will be saved.\n",
    "6. lr: default is 1e-5.\n",
    "7. lam: default is 1e-1, the inner parameter (Parameter alpha in paper).\n",
    "8. batch_size: default 256.\n",
    "9. epochs: default 200.\n",
    "10. patience: default 15, the patience for early stopping.\n",
    "11. lr_step: default [30,100], These are the milestones for the MultiStepLR setting, which adjusts the learning rate at specified epochs.\n",
    "12. encoderprofile_in_dim: default 5000. Adjust this parameter if the number of input genes differs from 5000.\n",
    "13. separatebatch: The default is False. If set to True, BCRs from different samples will be treated as distinct BCRs. Ensure that your BCR input file contains a \"sample\" column if you choose to enable this option."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The codes below return numpy arrays for BCR embeddings and gex embeddings. Meanwhile, it will output \"bcrembedding.csv\" and \"gexemedding.csv\" under the outdir you designated.  \n",
    "\n",
    "If CUDA raised error, this is due to a crush with the previous loaded model. Please restart the jupyter notebook and directly run the cell below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "learning rate is  1e-05\n",
      "Adjusting learning rate of group 0 to 1.0000e-05.\n",
      "Adjusting learning rate of group 0 to 1.0000e-05.\n",
      "Epoch:[0/1]\tloss:7.07274\tloss_cmc:3.472365\tloss_p2p:3.687132\tloss_b2b:0.002449\n"
     ]
    }
   ],
   "source": [
    "from CoMBCR.CoMBCR import CoMBCR_main\n",
    "\n",
    "bcremb, gexemb = CoMBCR_main(bcrpath=\"exampledata/example_bcr.csv\", \n",
    "            rnapath=\"exampledata/example_rna.csv\", \n",
    "            bcroriginal=\"exampledata/example_bcrori.csv\", \n",
    "            outdir=\"example_outdir\",\n",
    "            epochs=1,\n",
    "            batch_size=32,\n",
    "            encoderprofile_in_dim=5000)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1000, 256)"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bcremb.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1000, 256)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gexemb.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Read the output files \"bcrembedding.csv\" and \"gexembedding.csv\" located in the designated output directory. Please note that these CSV files directly store the numpy arrays and, as such, do not include any \"barcode\" column. When reading these files, ensure that you do not specify any index column."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "bcremb = pd.read_csv(\"example_outdir/Embeddings/bcrembeddings\")\n",
    "gexemb = pd.read_csv(\"example_outdir/Embeddings/gexembeddings\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
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       "      <td>0.029612</td>\n",
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       "      <td>-0.182125</td>\n",
       "      <td>0.023510</td>\n",
       "      <td>-0.041843</td>\n",
       "      <td>-0.049026</td>\n",
       "      <td>-0.042913</td>\n",
       "      <td>0.086104</td>\n",
       "      <td>-0.060631</td>\n",
       "      <td>-0.022182</td>\n",
       "      <td>0.026433</td>\n",
       "      <td>0.007512</td>\n",
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       "      <td>0.033859</td>\n",
       "      <td>0.027408</td>\n",
       "      <td>-0.012790</td>\n",
       "      <td>0.118991</td>\n",
       "      <td>0.037054</td>\n",
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       "      <td>-0.013472</td>\n",
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       "      <td>-0.018854</td>\n",
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       "      <td>0.080526</td>\n",
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       "      <td>0.001821</td>\n",
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       "4  0.013984 -0.057683 -0.067793  0.080526 -0.009838  0.049828  0.068106   \n",
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       "\n",
       "        250       251       252       253       254       255  \n",
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       "2 -0.042913  0.086104 -0.060631 -0.022182  0.026433  0.007512  \n",
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       "4 -0.009095  0.052927 -0.116035  0.022259 -0.001118 -0.014250  \n",
       "\n",
       "[5 rows x 256 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bcremb.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
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       "      <td>-0.033765</td>\n",
       "      <td>-0.051641</td>\n",
       "      <td>-0.003662</td>\n",
       "      <td>-0.027082</td>\n",
       "      <td>0.036087</td>\n",
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       "      <td>0.066959</td>\n",
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       "\n",
       "        250       251       252       253       254       255  \n",
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       "4 -0.039822 -0.060070  0.023413  0.028433  0.026463  0.055106  \n",
       "\n",
       "[5 rows x 256 columns]"
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     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gexemb.head()"
   ]
  }
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