iStar.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Anndata to  tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "\n",
    "cnt_tsv = pd.read_csv('./data/demo/cnts.tsv', sep='\\t')\n",
    "loc_raw_tsv = pd.read_csv('./data/demo/locs-raw.tsv', sep='\\t')\n",
    "celltype_tsv = pd.read_csv('./data/markers/celltype.tsv', sep='\\t')\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>spot</th>\n",
       "      <th>FO538757.1</th>\n",
       "      <th>SAMD11</th>\n",
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       "      <th>PLEKHN1</th>\n",
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       "      <th>HES4</th>\n",
       "      <th>ISG15</th>\n",
       "      <th>AGRN</th>\n",
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       "      <th>F8</th>\n",
       "      <th>FUNDC2</th>\n",
       "      <th>BRCC3</th>\n",
       "      <th>VBP1</th>\n",
       "      <th>CLIC2</th>\n",
       "      <th>SPRY3</th>\n",
       "      <th>VAMP7</th>\n",
       "      <th>USP9Y</th>\n",
       "      <th>TMSB4Y</th>\n",
       "      <th>NLGN4Y</th>\n",
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       "  </thead>\n",
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       "      <th>0</th>\n",
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       "      <td>10x11</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10x13</td>\n",
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       "      <td>1</td>\n",
       "      <td>4</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>10x14</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 14993 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    spot  FO538757.1  SAMD11  NOC2L  KLHL17  PLEKHN1  PERM1  HES4  ISG15  \\\n",
       "0  10x10           0       1      0       0        0      0     0      3   \n",
       "1  10x11           0       0      0       0        0      0     0      2   \n",
       "2  10x12           0       0      0       0        0      0     1      1   \n",
       "3  10x13           0       0      0       0        0      0     1      4   \n",
       "4  10x14           0       0      0       0        0      0     1      1   \n",
       "\n",
       "   AGRN  ...  F8  FUNDC2  BRCC3  VBP1  CLIC2  SPRY3  VAMP7  USP9Y  TMSB4Y  \\\n",
       "0     0  ...   0       0      0     0      0      0      0      0       0   \n",
       "1     0  ...   0       0      0     0      0      0      0      0       0   \n",
       "2     0  ...   0       0      0     1      0      0      0      0       0   \n",
       "3     0  ...   0       0      0     0      0      0      0      0       0   \n",
       "4     0  ...   0       0      0     0      0      0      0      0       0   \n",
       "\n",
       "   NLGN4Y  \n",
       "0       0  \n",
       "1       0  \n",
       "2       0  \n",
       "3       0  \n",
       "4       0  \n",
       "\n",
       "[5 rows x 14993 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cnt_tsv.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th>0</th>\n",
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       "      <td>14160.5</td>\n",
       "      <td>13648.0</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10x11</td>\n",
       "      <td>14150.5</td>\n",
       "      <td>12925.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10x12</td>\n",
       "      <td>14151.0</td>\n",
       "      <td>12195.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10x13</td>\n",
       "      <td>14126.0</td>\n",
       "      <td>11465.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>10x14</td>\n",
       "      <td>14138.5</td>\n",
       "      <td>10745.5</td>\n",
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      ],
      "text/plain": [
       "    spot        x        y\n",
       "0  10x10  14160.5  13648.0\n",
       "1  10x11  14150.5  12925.5\n",
       "2  10x12  14151.0  12195.5\n",
       "3  10x13  14126.0  11465.5\n",
       "4  10x14  14138.5  10745.5"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "loc_raw_tsv.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene</th>\n",
       "      <th>label</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ACKR1</td>\n",
       "      <td>Endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>FABP4</td>\n",
       "      <td>Endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>PLVAP</td>\n",
       "      <td>Endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>RAMP2</td>\n",
       "      <td>Endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>VWF</td>\n",
       "      <td>Endothelial</td>\n",
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       "  </tbody>\n",
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      ],
      "text/plain": [
       "    gene        label\n",
       "0  ACKR1  Endothelial\n",
       "1  FABP4  Endothelial\n",
       "2  PLVAP  Endothelial\n",
       "3  RAMP2  Endothelial\n",
       "4    VWF  Endothelial"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "celltype_tsv.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Start"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "output_dir ='/home/m264377/hwang_group/PUBLIC/lab_members/inyeop_jang/project/single_cell/istar/data/BS06-9313-8_Tumor'\n",
    "os.makedirs(output_dir,exist_ok=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/m264377/miniconda3/envs/singlecell/lib/python3.9/site-packages/anndata/_core/anndata.py:1840: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
      "  utils.warn_names_duplicates(\"var\")\n",
      "/home/m264377/miniconda3/envs/singlecell/lib/python3.9/site-packages/anndata/_core/anndata.py:1840: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
      "  utils.warn_names_duplicates(\"var\")\n"
     ]
    }
   ],
   "source": [
    "import scanpy as sc\n",
    "adata = sc.read_visium('/home/m264377/hwang_group/PUBLIC/Projects/U01_HTAN_GC_tumor_dev/RawData/10x_Visium/spaceranger_outs/BS06-9313-8_Tumor__3/outs/')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "      <th>pxl_col_in_fullres</th>\n",
       "      <th>pxl_row_in_fullres</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2464</th>\n",
       "      <td>AGGTAGGCAGGTGAGC-1</td>\n",
       "      <td>3863</td>\n",
       "      <td>856</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2465</th>\n",
       "      <td>ATCGCAGTATGTATTA-1</td>\n",
       "      <td>3829</td>\n",
       "      <td>856</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2466</th>\n",
       "      <td>ATGCTTGGACTACACG-1</td>\n",
       "      <td>3794</td>\n",
       "      <td>857</td>\n",
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       "      <td>TATTGAATCTCACGCC-1</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>11893</th>\n",
       "      <td>GGCGGTCACTTCTACA-1</td>\n",
       "      <td>3190</td>\n",
       "      <td>3370</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11894</th>\n",
       "      <td>ACCTGCACTAACGTTA-1</td>\n",
       "      <td>3156</td>\n",
       "      <td>3371</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11895</th>\n",
       "      <td>TGAGCAGATGGCTATG-1</td>\n",
       "      <td>3121</td>\n",
       "      <td>3371</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11896</th>\n",
       "      <td>GAAGCTTACCAAGGTG-1</td>\n",
       "      <td>3087</td>\n",
       "      <td>3372</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11897</th>\n",
       "      <td>GCAAGCAGTGCTAGCC-1</td>\n",
       "      <td>3052</td>\n",
       "      <td>3373</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6801 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  barcode  pxl_col_in_fullres  pxl_row_in_fullres\n",
       "2464   AGGTAGGCAGGTGAGC-1                3863                 856\n",
       "2465   ATCGCAGTATGTATTA-1                3829                 856\n",
       "2466   ATGCTTGGACTACACG-1                3794                 857\n",
       "2467   TATTGAATCTCACGCC-1                3760                 858\n",
       "2576   GGCTGAGTATCCATGA-1                3847                 886\n",
       "...                   ...                 ...                 ...\n",
       "11893  GGCGGTCACTTCTACA-1                3190                3370\n",
       "11894  ACCTGCACTAACGTTA-1                3156                3371\n",
       "11895  TGAGCAGATGGCTATG-1                3121                3371\n",
       "11896  GAAGCTTACCAAGGTG-1                3087                3372\n",
       "11897  GCAAGCAGTGCTAGCC-1                3052                3373\n",
       "\n",
       "[6801 rows x 3 columns]"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df1 = pd.read_csv('/home/m264377/hwang_group/PUBLIC/Projects/U01_HTAN_GC_tumor_dev/RawData/10x_Visium/spaceranger_outs/BS06-9313-8_Tumor__3/outs/spatial/tissue_positions.csv')\n",
    "df1=df1[(df1['in_tissue']==1) & (df1['pxl_col_in_fullres']>=0) & (df1['pxl_row_in_fullres'] >=0) ][['barcode','pxl_col_in_fullres', 'pxl_row_in_fullres']]\n",
    "df1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
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       "      <th>2465</th>\n",
       "      <td>ATCGCAGTATGTATTA-1</td>\n",
       "      <td>3829</td>\n",
       "      <td>856</td>\n",
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       "    <tr>\n",
       "      <th>2466</th>\n",
       "      <td>ATGCTTGGACTACACG-1</td>\n",
       "      <td>3794</td>\n",
       "      <td>857</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2467</th>\n",
       "      <td>TATTGAATCTCACGCC-1</td>\n",
       "      <td>3760</td>\n",
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       "    <tr>\n",
       "      <th>2576</th>\n",
       "      <td>GGCTGAGTATCCATGA-1</td>\n",
       "      <td>3847</td>\n",
       "      <td>886</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11893</th>\n",
       "      <td>GGCGGTCACTTCTACA-1</td>\n",
       "      <td>3190</td>\n",
       "      <td>3370</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11894</th>\n",
       "      <td>ACCTGCACTAACGTTA-1</td>\n",
       "      <td>3156</td>\n",
       "      <td>3371</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11895</th>\n",
       "      <td>TGAGCAGATGGCTATG-1</td>\n",
       "      <td>3121</td>\n",
       "      <td>3371</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11896</th>\n",
       "      <td>GAAGCTTACCAAGGTG-1</td>\n",
       "      <td>3087</td>\n",
       "      <td>3372</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11897</th>\n",
       "      <td>GCAAGCAGTGCTAGCC-1</td>\n",
       "      <td>3052</td>\n",
       "      <td>3373</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6801 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                     spot     x     y\n",
       "2464   AGGTAGGCAGGTGAGC-1  3863   856\n",
       "2465   ATCGCAGTATGTATTA-1  3829   856\n",
       "2466   ATGCTTGGACTACACG-1  3794   857\n",
       "2467   TATTGAATCTCACGCC-1  3760   858\n",
       "2576   GGCTGAGTATCCATGA-1  3847   886\n",
       "...                   ...   ...   ...\n",
       "11893  GGCGGTCACTTCTACA-1  3190  3370\n",
       "11894  ACCTGCACTAACGTTA-1  3156  3371\n",
       "11895  TGAGCAGATGGCTATG-1  3121  3371\n",
       "11896  GAAGCTTACCAAGGTG-1  3087  3372\n",
       "11897  GCAAGCAGTGCTAGCC-1  3052  3373\n",
       "\n",
       "[6801 rows x 3 columns]"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df1_out =df1.rename(columns={\"barcode\":\"spot\", \"pxl_col_in_fullres\":\"x\", \"pxl_row_in_fullres\":\"y\"})\n",
    "# df1_out.to_csv(f'{output_dir}/locs-raw.tsv', sep='\\t', index=False)\n",
    "df1_out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index([ 2464,  2465,  2466,  2467,  2576,  2577,  2578,  2579,  2580,  2581,\n",
       "       ...\n",
       "       11782, 11783, 11784, 11785, 11892, 11893, 11894, 11895, 11896, 11897],\n",
       "      dtype='int64', length=6801)"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df1_out.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.DataFrame(adata.X.toarray(),columns=adata.var_names)\n",
    "df.insert(loc=0, column='spot', value=adata.obs_names)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "    }\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>spot</th>\n",
       "      <th>SAMD11</th>\n",
       "      <th>NOC2L</th>\n",
       "      <th>KLHL17</th>\n",
       "      <th>PLEKHN1</th>\n",
       "      <th>PERM1</th>\n",
       "      <th>HES4</th>\n",
       "      <th>ISG15</th>\n",
       "      <th>AGRN</th>\n",
       "      <th>RNF223</th>\n",
       "      <th>...</th>\n",
       "      <th>MT-ND2</th>\n",
       "      <th>MT-CO2</th>\n",
       "      <th>MT-ATP6</th>\n",
       "      <th>MT-CO3</th>\n",
       "      <th>MT-ND3</th>\n",
       "      <th>MT-ND4L</th>\n",
       "      <th>MT-ND4</th>\n",
       "      <th>MT-ND5</th>\n",
       "      <th>MT-ND6</th>\n",
       "      <th>MT-CYB</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AACAATCCGAGTGGAC-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AACAATGGAACCACAT-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>10.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>18.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AACACCAGCCTACTCG-1</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>41.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>43.0</td>\n",
       "      <td>70.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AACACCATTCGCATAC-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>26.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>26.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>35.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AACACCGAATGTCTCA-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>44.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>62.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>43.0</td>\n",
       "      <td>70.0</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>6796</th>\n",
       "      <td>TGTTGGCCAATATGGC-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6797</th>\n",
       "      <td>TGTTGGCCTGTAGCGG-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>10.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6798</th>\n",
       "      <td>TGTTGGTGAGCGGACG-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6799</th>\n",
       "      <td>TGTTGGTGCGCTTCGC-1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>77.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>60.0</td>\n",
       "      <td>101.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>78.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>60.0</td>\n",
       "      <td>99.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6800</th>\n",
       "      <td>TGTTGGTGCGGAATCA-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>13.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6801 rows × 18086 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    spot  SAMD11  NOC2L  KLHL17  PLEKHN1  PERM1  HES4  ISG15  \\\n",
       "0     AACAATCCGAGTGGAC-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "1     AACAATGGAACCACAT-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "2     AACACCAGCCTACTCG-1     2.0    2.0     0.0      0.0    0.0   0.0    1.0   \n",
       "3     AACACCATTCGCATAC-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "4     AACACCGAATGTCTCA-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "...                  ...     ...    ...     ...      ...    ...   ...    ...   \n",
       "6796  TGTTGGCCAATATGGC-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6797  TGTTGGCCTGTAGCGG-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6798  TGTTGGTGAGCGGACG-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6799  TGTTGGTGCGCTTCGC-1     1.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6800  TGTTGGTGCGGAATCA-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "\n",
       "      AGRN  RNF223  ...  MT-ND2  MT-CO2  MT-ATP6  MT-CO3  MT-ND3  MT-ND4L  \\\n",
       "0      0.0     0.0  ...     1.0     2.0      2.0     3.0     1.0      0.0   \n",
       "1      0.0     0.0  ...    10.0    14.0      8.0    18.0    11.0     14.0   \n",
       "2      2.0     0.0  ...    41.0    38.0     34.0    67.0    16.0     61.0   \n",
       "3      0.0     0.0  ...    26.0    21.0     19.0    19.0    14.0     12.0   \n",
       "4      0.0     0.0  ...    44.0    31.0     40.0    69.0    28.0     62.0   \n",
       "...    ...     ...  ...     ...     ...      ...     ...     ...      ...   \n",
       "6796   0.0     0.0  ...     0.0     1.0      0.0     1.0     0.0      0.0   \n",
       "6797   0.0     0.0  ...    10.0     5.0      8.0    16.0     4.0     10.0   \n",
       "6798   0.0     0.0  ...     2.0     4.0      3.0    10.0     3.0      8.0   \n",
       "6799   3.0     0.0  ...    77.0    56.0     60.0   101.0    56.0     69.0   \n",
       "6800   1.0     0.0  ...     7.0    10.0      7.0    13.0     4.0     10.0   \n",
       "\n",
       "      MT-ND4  MT-ND5  MT-ND6  MT-CYB  \n",
       "0        0.0     1.0     1.0     3.0  \n",
       "1       19.0    11.0    14.0    18.0  \n",
       "2       38.0    34.0    43.0    70.0  \n",
       "3       26.0    21.0    15.0    35.0  \n",
       "4       57.0    32.0    43.0    70.0  \n",
       "...      ...     ...     ...     ...  \n",
       "6796     1.0     0.0     1.0     1.0  \n",
       "6797     7.0     7.0     7.0    20.0  \n",
       "6798     5.0     0.0     3.0     5.0  \n",
       "6799    78.0    56.0    60.0    99.0  \n",
       "6800     7.0     3.0     6.0    13.0  \n",
       "\n",
       "[6801 rows x 18086 columns]"
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>spot</th>\n",
       "      <th>SAMD11</th>\n",
       "      <th>NOC2L</th>\n",
       "      <th>KLHL17</th>\n",
       "      <th>PLEKHN1</th>\n",
       "      <th>PERM1</th>\n",
       "      <th>HES4</th>\n",
       "      <th>ISG15</th>\n",
       "      <th>AGRN</th>\n",
       "      <th>RNF223</th>\n",
       "      <th>...</th>\n",
       "      <th>MT-ND2</th>\n",
       "      <th>MT-CO2</th>\n",
       "      <th>MT-ATP6</th>\n",
       "      <th>MT-CO3</th>\n",
       "      <th>MT-ND3</th>\n",
       "      <th>MT-ND4L</th>\n",
       "      <th>MT-ND4</th>\n",
       "      <th>MT-ND5</th>\n",
       "      <th>MT-ND6</th>\n",
       "      <th>MT-CYB</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AACAATCCGAGTGGAC-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AACAATGGAACCACAT-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>10.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>18.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AACACCAGCCTACTCG-1</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>41.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>43.0</td>\n",
       "      <td>70.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AACACCATTCGCATAC-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>26.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>26.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>35.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AACACCGAATGTCTCA-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>44.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>62.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>43.0</td>\n",
       "      <td>70.0</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>6796</th>\n",
       "      <td>TGTTGGCCAATATGGC-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6797</th>\n",
       "      <td>TGTTGGCCTGTAGCGG-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>10.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6798</th>\n",
       "      <td>TGTTGGTGAGCGGACG-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6799</th>\n",
       "      <td>TGTTGGTGCGCTTCGC-1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>77.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>60.0</td>\n",
       "      <td>101.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>78.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>60.0</td>\n",
       "      <td>99.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6800</th>\n",
       "      <td>TGTTGGTGCGGAATCA-1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>13.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6801 rows × 18086 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    spot  SAMD11  NOC2L  KLHL17  PLEKHN1  PERM1  HES4  ISG15  \\\n",
       "0     AACAATCCGAGTGGAC-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "1     AACAATGGAACCACAT-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "2     AACACCAGCCTACTCG-1     2.0    2.0     0.0      0.0    0.0   0.0    1.0   \n",
       "3     AACACCATTCGCATAC-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "4     AACACCGAATGTCTCA-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "...                  ...     ...    ...     ...      ...    ...   ...    ...   \n",
       "6796  TGTTGGCCAATATGGC-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6797  TGTTGGCCTGTAGCGG-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6798  TGTTGGTGAGCGGACG-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6799  TGTTGGTGCGCTTCGC-1     1.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "6800  TGTTGGTGCGGAATCA-1     0.0    0.0     0.0      0.0    0.0   0.0    0.0   \n",
       "\n",
       "      AGRN  RNF223  ...  MT-ND2  MT-CO2  MT-ATP6  MT-CO3  MT-ND3  MT-ND4L  \\\n",
       "0      0.0     0.0  ...     1.0     2.0      2.0     3.0     1.0      0.0   \n",
       "1      0.0     0.0  ...    10.0    14.0      8.0    18.0    11.0     14.0   \n",
       "2      2.0     0.0  ...    41.0    38.0     34.0    67.0    16.0     61.0   \n",
       "3      0.0     0.0  ...    26.0    21.0     19.0    19.0    14.0     12.0   \n",
       "4      0.0     0.0  ...    44.0    31.0     40.0    69.0    28.0     62.0   \n",
       "...    ...     ...  ...     ...     ...      ...     ...     ...      ...   \n",
       "6796   0.0     0.0  ...     0.0     1.0      0.0     1.0     0.0      0.0   \n",
       "6797   0.0     0.0  ...    10.0     5.0      8.0    16.0     4.0     10.0   \n",
       "6798   0.0     0.0  ...     2.0     4.0      3.0    10.0     3.0      8.0   \n",
       "6799   3.0     0.0  ...    77.0    56.0     60.0   101.0    56.0     69.0   \n",
       "6800   1.0     0.0  ...     7.0    10.0      7.0    13.0     4.0     10.0   \n",
       "\n",
       "      MT-ND4  MT-ND5  MT-ND6  MT-CYB  \n",
       "0        0.0     1.0     1.0     3.0  \n",
       "1       19.0    11.0    14.0    18.0  \n",
       "2       38.0    34.0    43.0    70.0  \n",
       "3       26.0    21.0    15.0    35.0  \n",
       "4       57.0    32.0    43.0    70.0  \n",
       "...      ...     ...     ...     ...  \n",
       "6796     1.0     0.0     1.0     1.0  \n",
       "6797     7.0     7.0     7.0    20.0  \n",
       "6798     5.0     0.0     3.0     5.0  \n",
       "6799    78.0    56.0    60.0    99.0  \n",
       "6800     7.0     3.0     6.0    13.0  \n",
       "\n",
       "[6801 rows x 18086 columns]"
      ]
     },
     "execution_count": 63,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.DataFrame(adata.X.toarray(),columns=adata.var_names)\n",
    "df.insert(loc=0, column='spot', value=adata.obs_names)\n",
    "df=df[df['spot'].isin(df1_out['spot'])].reset_index(drop=True)\n",
    "df.sort_values(by='spot', inplace=True)\n",
    "df.to_csv(f'{output_dir}/cnts.tsv', sep='\\t', index=False)\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "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>spot</th>\n",
       "      <th>x</th>\n",
       "      <th>y</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AACAATCCGAGTGGAC-1</td>\n",
       "      <td>3102</td>\n",
       "      <td>3282</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AACAATGGAACCACAT-1</td>\n",
       "      <td>3331</td>\n",
       "      <td>1819</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AACACCAGCCTACTCG-1</td>\n",
       "      <td>3198</td>\n",
       "      <td>1137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AACACCATTCGCATAC-1</td>\n",
       "      <td>1490</td>\n",
       "      <td>1825</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AACACCGAATGTCTCA-1</td>\n",
       "      <td>842</td>\n",
       "      <td>1273</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6796</th>\n",
       "      <td>TGTTGGCCAATATGGC-1</td>\n",
       "      <td>118</td>\n",
       "      <td>2091</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6797</th>\n",
       "      <td>TGTTGGCCTGTAGCGG-1</td>\n",
       "      <td>2532</td>\n",
       "      <td>1418</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6798</th>\n",
       "      <td>TGTTGGTGAGCGGACG-1</td>\n",
       "      <td>3592</td>\n",
       "      <td>1962</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6799</th>\n",
       "      <td>TGTTGGTGCGCTTCGC-1</td>\n",
       "      <td>1687</td>\n",
       "      <td>1345</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6800</th>\n",
       "      <td>TGTTGGTGCGGAATCA-1</td>\n",
       "      <td>2402</td>\n",
       "      <td>2701</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6801 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    spot     x     y\n",
       "0     AACAATCCGAGTGGAC-1  3102  3282\n",
       "1     AACAATGGAACCACAT-1  3331  1819\n",
       "2     AACACCAGCCTACTCG-1  3198  1137\n",
       "3     AACACCATTCGCATAC-1  1490  1825\n",
       "4     AACACCGAATGTCTCA-1   842  1273\n",
       "...                  ...   ...   ...\n",
       "6796  TGTTGGCCAATATGGC-1   118  2091\n",
       "6797  TGTTGGCCTGTAGCGG-1  2532  1418\n",
       "6798  TGTTGGTGAGCGGACG-1  3592  1962\n",
       "6799  TGTTGGTGCGCTTCGC-1  1687  1345\n",
       "6800  TGTTGGTGCGGAATCA-1  2402  2701\n",
       "\n",
       "[6801 rows x 3 columns]"
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "df1_out=df1_out[df1_out['spot'].isin(df['spot'])].reset_index(drop=True)\n",
    "df1_out.sort_values(by='spot', inplace=True)\n",
    "df1_out.to_csv(f'{output_dir}/locs-raw.tsv', sep='\\t', index=False)\n",
    "df1_out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 65,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "(df.index==df1_out.index).all()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import json\n",
    "with open('/home/m264377/hwang_group/PUBLIC/Projects/U01_HTAN_GC_tumor_dev/RawData/10x_Visium/spaceranger_outs/BS06-9313-8_Tumor__3/outs/spatial/scalefactors_json.json') as f:\n",
    "    scalefactors = json.load(f)\n",
    "    spot_radius_fullres = float(scalefactors['spot_diameter_fullres'])\n",
    "\n",
    "with open(f'{output_dir}/radius-raw.txt', 'w') as f:\n",
    "    f.write(str(spot_radius_fullres*0.5))\n",
    "\n",
    "\n",
    "with open(f'{output_dir}/pixel-size-raw.txt', 'w') as f:\n",
    "    f.write(str(55/spot_radius_fullres))\n",
    "\n",
    "\n",
    "import tifffile\n",
    "import cv2\n",
    "tif = tifffile.imread('/home/m264377/hwang_group/PUBLIC/Projects/U01_HTAN_GC_tumor_dev/RawData/HE_images/CROP/BS06-9313-8_Tumor__3__ROI.tiff')\n",
    "cv2.imwrite(f'{output_dir}/he-raw.jpg', cv2.cvtColor(tif[:,:,0:3],cv2.COLOR_BGR2RGB), [int(cv2.IMWRITE_JPEG_QUALITY), 100])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "10.324346529527679"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "20.648693059055358*0.5"
   ]
  }
 ],
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