{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 5_ctx_th_gene_analysis" ] }, { "cell_type": "code", "execution_count": 62, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import anndata\n", "import scanpy as sc\n", "from tqdm import tqdm\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", "import warnings\n", "from scipy.stats import pearsonr\n", "import seaborn as sns\n", "import os\n", "from matplotlib.patches import Patch\n", "import matplotlib as mpl\n", "mpl.rcParams['pdf.fonttype'] = 42\n", "mpl.rcParams['ps.fonttype'] = 42\n", "warnings.filterwarnings('ignore')" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "ctx_regions = ['ACAd', 'ACAv', 'PL', 'ILA', 'ORBl', 'ORBvl', 'AId', 'SSs', 'SSp-bfd', 'SSp-ll', 'SSp-ul', 'SSp-n', 'SSp-m', 'MOp',\n", " 'MOs', 'VISal', 'VISl', 'VISp', 'VISpor', 'VISrl', 'VISam', 'VISpm', 'RSPd', 'RSPv', 'AUDp']\n", "th_regions = ['VPL', 'VPM', 'PO', 'PoT', 'VPMpc', 'VPLpc', 'SPFp',\n", " 'MG', 'PIL', 'PP', 'SGN', 'AD', 'AV', 'LD', 'LP', 'VAL', 'PF', 'CL',\n", " 'SubG', 'LGv', 'IGL', 'POL', 'MD', 'IMD', 'CM', 'SMT',\n", " 'SPA', 'VM', 'PCN', 'PVT', 'PT', 'RE', 'SPFm', 'Xi', 'RH', 'IAM', 'PR',\n", " 'LH', 'MH', 'IAD', 'RT']" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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133403 rows × 9 columns
\n", "| \n", " | VPL | \n", "VPM | \n", "PO | \n", "PoT | \n", "VPMpc | \n", "VPLpc | \n", "SPFp | \n", "PIL | \n", "PP | \n", "SGN | \n", "... | \n", "PT | \n", "RE | \n", "SPFm | \n", "RH | \n", "IAM | \n", "PR | \n", "LH | \n", "MH | \n", "IAD | \n", "RT | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| anchor source | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| ACAd | \n", "-1.090171 | \n", "-6.342319 | \n", "-5.426504 | \n", "-5.605730 | \n", "-6.008217 | \n", "-10.000000 | \n", "-5.566647 | \n", "-5.895726 | \n", "-2.527515 | \n", "-10.000000 | \n", "... | \n", "-2.727347 | \n", "-1.183582 | \n", "-1.670217 | \n", "-1.755893 | \n", "-1.809540 | \n", "-1.685012 | \n", "-1.448781 | \n", "-6.879172 | \n", "-1.144436 | \n", "-0.769605 | \n", "
| ACAv | \n", "-1.423084 | \n", "-10.000000 | \n", "-10.000000 | \n", "-5.608990 | \n", "-1.929727 | \n", "-10.000000 | \n", "-1.132599 | \n", "-5.927264 | \n", "-2.399007 | \n", "-10.000000 | \n", "... | \n", "-1.873386 | \n", "-1.182032 | \n", "-1.403915 | \n", "-1.655801 | \n", "-1.468856 | \n", "-1.057059 | \n", "-5.430204 | \n", "-10.000000 | \n", "-0.900422 | \n", "-0.413475 | \n", "
| PL | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-5.992111 | \n", "-10.000000 | \n", "-5.882870 | \n", "-5.961731 | \n", "-10.000000 | \n", "-10.000000 | \n", "... | \n", "-1.389215 | \n", "-0.970923 | \n", "-5.878069 | \n", "-1.704030 | \n", "-1.890465 | \n", "-1.035770 | \n", "-1.639700 | \n", "-10.000000 | \n", "-1.569406 | \n", "-0.807789 | \n", "
| ILA | \n", "-6.325188 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-6.017124 | \n", "-10.000000 | \n", "-5.751314 | \n", "-2.520655 | \n", "-6.144408 | \n", "-6.509481 | \n", "... | \n", "-0.546665 | \n", "-0.545810 | \n", "-1.654686 | \n", "-1.603711 | \n", "-1.813752 | \n", "-0.737798 | \n", "-1.087582 | \n", "-1.804623 | \n", "-1.274479 | \n", "-0.642914 | \n", "
| ORBl | \n", "-6.224208 | \n", "-6.003722 | \n", "-5.437890 | \n", "-10.000000 | \n", "-1.905725 | \n", "-10.000000 | \n", "-5.918426 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "... | \n", "-2.467256 | \n", "-1.554422 | \n", "-6.000569 | \n", "-1.589246 | \n", "-2.697192 | \n", "-5.901769 | \n", "-1.834357 | \n", "-10.000000 | \n", "-2.160936 | \n", "-0.693127 | \n", "
| ORBvl | \n", "-5.882161 | \n", "-10.000000 | \n", "-10.000000 | \n", "-6.375555 | \n", "-2.185265 | \n", "-10.000000 | \n", "-5.950850 | \n", "-6.211784 | \n", "-10.000000 | \n", "-6.643945 | \n", "... | \n", "-0.828830 | \n", "-0.776871 | \n", "-5.913809 | \n", "-1.420968 | \n", "-1.698088 | \n", "-0.956903 | \n", "-1.414943 | \n", "-6.478384 | \n", "-5.357311 | \n", "-0.545583 | \n", "
| AId | \n", "-10.000000 | \n", "-5.641845 | \n", "-5.325552 | \n", "-6.050576 | \n", "-1.452111 | \n", "-6.043647 | \n", "-6.252712 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "... | \n", "-2.700659 | \n", "-5.744953 | \n", "-5.990823 | \n", "-2.209329 | \n", "-6.914940 | \n", "-5.937606 | \n", "-3.096440 | \n", "-10.000000 | \n", "-10.000000 | \n", "-5.233617 | \n", "
| SSs | \n", "-0.533973 | \n", "-0.245893 | \n", "-0.284354 | \n", "-1.007490 | \n", "-1.754370 | \n", "-5.729620 | \n", "-3.632334 | \n", "-5.785201 | \n", "-7.888268 | \n", "-5.437407 | \n", "... | \n", "-10.000000 | \n", "-4.436421 | \n", "-4.193741 | \n", "-4.288500 | \n", "-8.377699 | \n", "-8.356392 | \n", "-6.792026 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.683757 | \n", "
| SSp-bfd | \n", "-5.483834 | \n", "-0.286921 | \n", "-0.440568 | \n", "-1.150783 | \n", "-6.616602 | \n", "-10.000000 | \n", "-2.125942 | \n", "-5.626288 | \n", "-5.918936 | \n", "-1.722711 | \n", "... | \n", "-10.000000 | \n", "-6.576067 | \n", "-3.461558 | \n", "-3.051209 | \n", "-10.000000 | \n", "-6.952895 | \n", "-10.000000 | \n", "-10.000000 | \n", "-3.256035 | \n", "-0.630895 | \n", "
| SSp-ll | \n", "-0.424806 | \n", "-0.984444 | \n", "-0.714249 | \n", "-1.830208 | \n", "-6.880859 | \n", "-10.000000 | \n", "-5.680297 | \n", "-5.937618 | \n", "-10.000000 | \n", "-2.661697 | \n", "... | \n", "-10.000000 | \n", "-2.811056 | \n", "-6.272099 | \n", "-3.059279 | \n", "-10.000000 | \n", "-10.000000 | \n", "-2.820684 | \n", "-10.000000 | \n", "-3.891500 | \n", "-0.704974 | \n", "
| SSp-ul | \n", "-0.512134 | \n", "-4.997219 | \n", "-0.126221 | \n", "-1.606216 | \n", "-1.955906 | \n", "-2.141609 | \n", "-5.729040 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "... | \n", "-10.000000 | \n", "-6.455041 | \n", "-10.000000 | \n", "-3.065086 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.765330 | \n", "
| SSp-n | \n", "-0.563616 | \n", "-0.029009 | \n", "-0.229639 | \n", "-1.545879 | \n", "-2.328005 | \n", "-2.089110 | \n", "-5.543640 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "... | \n", "-10.754420 | \n", "-6.051322 | \n", "-6.353382 | \n", "-2.713103 | \n", "-10.000000 | \n", "-6.398222 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.544709 | \n", "
| SSp-m | \n", "-0.538166 | \n", "0.065971 | \n", "-0.230394 | \n", "-5.600657 | \n", "-1.676116 | \n", "-6.019576 | \n", "-10.000000 | \n", "-6.087167 | \n", "-10.000000 | \n", "-10.000000 | \n", "... | \n", "-10.000000 | \n", "-6.391604 | \n", "-10.754420 | \n", "-6.380348 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.589138 | \n", "
| MOp | \n", "-0.129938 | \n", "-5.183974 | \n", "-0.205113 | \n", "-5.752578 | \n", "-6.204141 | \n", "-6.578336 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-2.334184 | \n", "... | \n", "-10.000000 | \n", "-6.272292 | \n", "-6.135587 | \n", "-6.590445 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.459391 | \n", "
| MOs | \n", "-0.818288 | \n", "-0.664884 | \n", "-0.153652 | \n", "-3.602665 | \n", "-3.845986 | \n", "-4.315142 | \n", "-3.629701 | \n", "-6.234426 | \n", "-8.224540 | \n", "-6.119077 | \n", "... | \n", "-10.000000 | \n", "-1.882719 | \n", "-8.014224 | \n", "-1.730154 | \n", "-4.054899 | \n", "-7.984730 | \n", "-6.475172 | \n", "-10.000000 | \n", "-4.038434 | \n", "-2.843340 | \n", "
| VISal | \n", "-1.034583 | \n", "-5.354679 | \n", "-0.599560 | \n", "-5.774497 | \n", "-6.619113 | \n", "-10.000000 | \n", "-2.364640 | \n", "-1.993791 | \n", "-5.664126 | \n", "-1.134140 | \n", "... | \n", "-10.000000 | \n", "-6.173552 | \n", "-6.443739 | \n", "-2.782023 | \n", "-6.598952 | \n", "-2.466052 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.740894 | \n", "
| VISl | \n", "-5.777306 | \n", "-5.321867 | \n", "-1.004276 | \n", "-5.966014 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-5.907370 | \n", "-5.862698 | \n", "-5.799969 | \n", "... | \n", "-10.000000 | \n", "-6.257293 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-6.888282 | \n", "-10.000000 | \n", "-6.836267 | \n", "-0.577579 | \n", "
| VISp | \n", "-1.422962 | \n", "-5.804932 | \n", "-5.833879 | \n", "-6.346772 | \n", "-10.754420 | \n", "-10.000000 | \n", "-10.000000 | \n", "-6.621287 | \n", "-10.000000 | \n", "-1.955335 | \n", "... | \n", "-10.000000 | \n", "-6.214321 | \n", "-10.000000 | \n", "-6.558477 | \n", "-6.892084 | \n", "-6.579267 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.617637 | \n", "
| VISpor | \n", "-2.192462 | \n", "-2.376547 | \n", "-5.726122 | \n", "-2.671269 | \n", "-7.021998 | \n", "-7.002497 | \n", "-10.000000 | \n", "-2.298210 | \n", "-6.092443 | \n", "-1.422456 | \n", "... | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.754420 | \n", "-6.612503 | \n", "-6.340301 | \n", "-10.000000 | \n", "-10.000000 | \n", "-1.387643 | \n", "
| VISrl | \n", "-0.791890 | \n", "-0.535124 | \n", "-0.339014 | \n", "-1.277799 | \n", "-10.000000 | \n", "-10.000000 | \n", "-5.761978 | \n", "-2.823176 | \n", "-6.031412 | \n", "-1.422637 | \n", "... | \n", "-10.000000 | \n", "-2.532333 | \n", "-6.264313 | \n", "-6.090899 | \n", "-6.429685 | \n", "-6.377060 | \n", "-10.000000 | \n", "-10.000000 | \n", "-6.126003 | \n", "-0.644216 | \n", "
| VISam | \n", "-0.527118 | \n", "-5.517881 | \n", "-0.478789 | \n", "-1.373619 | \n", "-10.000000 | \n", "-10.000000 | \n", "-2.186025 | \n", "-5.816067 | \n", "-5.942121 | \n", "-1.356229 | \n", "... | \n", "-6.514253 | \n", "-1.600301 | \n", "-6.087990 | \n", "-2.147693 | \n", "-3.042415 | \n", "-1.905533 | \n", "-2.012084 | \n", "-6.859115 | \n", "-1.975844 | \n", "-0.398044 | \n", "
| VISpm | \n", "-0.916817 | \n", "-5.587206 | \n", "-1.151516 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-6.169564 | \n", "-5.918708 | \n", "-10.000000 | \n", "-6.051864 | \n", "... | \n", "-6.427577 | \n", "-1.872311 | \n", "-6.168127 | \n", "-2.308679 | \n", "-4.021444 | \n", "-2.168330 | \n", "-10.000000 | \n", "-10.000000 | \n", "-5.965749 | \n", "-0.397564 | \n", "
| RSPd | \n", "-5.670737 | \n", "-10.000000 | \n", "-5.986022 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-5.812420 | \n", "-5.987416 | \n", "-6.104530 | \n", "-10.000000 | \n", "... | \n", "-10.000000 | \n", "-6.027620 | \n", "-6.161968 | \n", "-2.701966 | \n", "-5.965488 | \n", "-6.153988 | \n", "-5.932982 | \n", "-10.000000 | \n", "-6.228290 | \n", "-0.731420 | \n", "
| RSPv | \n", "-1.311758 | \n", "-10.000000 | \n", "-10.000000 | \n", "-10.000000 | \n", "-7.055145 | \n", "-10.000000 | \n", "-10.000000 | \n", "-2.714168 | \n", "-3.050242 | \n", "-10.000000 | \n", "... | \n", "-10.000000 | \n", "-2.677701 | \n", "-2.675464 | \n", "-6.199900 | \n", "-5.892359 | \n", "-10.000000 | \n", "-6.172558 | \n", "-10.000000 | \n", "-5.758051 | \n", "-0.739684 | \n", "
| AUDp | \n", "-5.334003 | \n", "-5.230048 | \n", "-5.778810 | \n", "-1.208616 | \n", "-10.000000 | \n", "-10.000000 | \n", "-2.475106 | \n", "-1.604605 | \n", "-5.675994 | \n", "-0.896259 | \n", "... | \n", "-10.000000 | \n", "-2.779426 | \n", "-6.144770 | \n", "-10.000000 | \n", "-10.000000 | \n", "-6.260222 | \n", "-6.894197 | \n", "-10.000000 | \n", "-10.000000 | \n", "-0.885349 | \n", "
25 rows × 37 columns
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|---|---|---|---|---|---|---|---|---|---|---|
| cell_label | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| 207252950882079766503645227815929952400 | \n", "Zhuang-ABCA-3.023 | \n", "50.597984 | \n", "41.393473 | \n", "12.239274 | \n", "5.059798 | \n", "4.139347 | \n", "1.223927 | \n", "SSs2/3 | \n", "01 IT-ET Glut | \n", "nan | \n", "
| 311894855078226645952213910865897976013 | \n", "Zhuang-ABCA-3.023 | \n", "50.420950 | \n", "41.271525 | \n", "12.251970 | \n", "5.042095 | \n", "4.127152 | \n", "1.225197 | \n", "SSs1 | \n", "01 IT-ET Glut | \n", "nan | \n", "
| 125208524519663791324346814779771999476 | \n", "Zhuang-ABCA-3.023 | \n", "50.959183 | \n", "43.276307 | \n", "12.158869 | \n", "5.095918 | \n", "4.327631 | \n", "1.215887 | \n", "SSs2/3 | \n", "01 IT-ET Glut | \n", "nan | \n", "
| 12594778395225515056477813574460470379 | \n", "Zhuang-ABCA-3.023 | \n", "49.836112 | \n", "42.209685 | \n", "12.238386 | \n", "4.983611 | \n", "4.220968 | \n", "1.223839 | \n", "SSs1 | \n", "01 IT-ET Glut | \n", "nan | \n", "
| 148621603142722639702356861951538418099 | \n", "Zhuang-ABCA-3.023 | \n", "51.023440 | \n", "42.722536 | \n", "12.174236 | \n", "5.102344 | \n", "4.272254 | \n", "1.217424 | \n", "SSs2/3 | \n", "01 IT-ET Glut | \n", "nan | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 137125155786416424728071422508382942054 | \n", "Zhuang-ABCA-3.009 | \n", "86.480430 | \n", "34.094203 | \n", "37.248728 | \n", "8.648043 | \n", "3.409420 | \n", "3.724873 | \n", "SGN | \n", "19 MB Glut | \n", "nan | \n", "
| 186321231466624970722021094909324401885 | \n", "Zhuang-ABCA-3.009 | \n", "86.443977 | \n", "35.015822 | \n", "37.291043 | \n", "8.644398 | \n", "3.501582 | \n", "3.729104 | \n", "POL | \n", "19 MB Glut | \n", "nan | \n", "
| 262284519603134366801326445274337827961 | \n", "Zhuang-ABCA-3.009 | \n", "86.388989 | \n", "32.866518 | \n", "37.212756 | \n", "8.638899 | \n", "3.286652 | \n", "3.721276 | \n", "SGN | \n", "19 MB Glut | \n", "nan | \n", "
| 33608739852097367198466784523454261485 | \n", "Zhuang-ABCA-3.009 | \n", "86.904204 | \n", "34.752896 | \n", "37.268567 | \n", "8.690420 | \n", "3.475290 | \n", "3.726857 | \n", "POL | \n", "19 MB Glut | \n", "nan | \n", "
| 303385550649730012456703013017610179856 | \n", "Zhuang-ABCA-3.009 | \n", "88.389510 | \n", "37.024369 | \n", "37.400811 | \n", "8.838951 | \n", "3.702437 | \n", "3.740081 | \n", "POL | \n", "19 MB Glut | \n", "nan | \n", "
133403 rows × 10 columns
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|---|---|---|---|---|---|---|---|---|---|---|
| cell_label | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| 188052700459908704250468015984246340174 | \n", "Zhuang-ABCA-3.017 | \n", "78.511319 | \n", "17.025034 | \n", "23.450480 | \n", "7.851132 | \n", "1.702503 | \n", "2.345048 | \n", "VISrl5 | \n", "01 IT-ET Glut | \n", "Visual | \n", "
| 244536282695664703731093924351585311804 | \n", "Zhuang-ABCA-3.017 | \n", "78.839495 | \n", "17.453570 | \n", "23.457475 | \n", "7.883949 | \n", "1.745357 | \n", "2.345747 | \n", "VISrl5 | \n", "01 IT-ET Glut | \n", "Visual | \n", "
| 207737713088111645489974231015219723398 | \n", "Zhuang-ABCA-3.017 | \n", "78.672275 | \n", "18.071984 | \n", "23.473123 | \n", "7.867227 | \n", "1.807198 | \n", "2.347312 | \n", "VISrl6a | \n", "01 IT-ET Glut | \n", "Visual | \n", "
| 282030992965481098907637606735824510623 | \n", "Zhuang-ABCA-3.017 | \n", "78.575583 | \n", "19.064710 | \n", "23.497188 | \n", "7.857558 | \n", "1.906471 | \n", "2.349719 | \n", "VISal6a | \n", "02 NP-CT-L6b Glut | \n", "Visual | \n", "
| 97661006042925800380741778764498794751 | \n", "Zhuang-ABCA-3.017 | \n", "78.796093 | \n", "19.073735 | \n", "23.494524 | \n", "7.879609 | \n", "1.907373 | \n", "2.349452 | \n", "VISal6a | \n", "02 NP-CT-L6b Glut | \n", "Visual | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 156947303650960194776993747274328011056 | \n", "Zhuang-ABCA-3.009 | \n", "84.812512 | \n", "30.863025 | \n", "37.253313 | \n", "8.481251 | \n", "3.086302 | \n", "3.725331 | \n", "LP | \n", "18 TH Glut | \n", "connected | \n", "
| 172268668275251998778345610664715788667 | \n", "Zhuang-ABCA-3.009 | \n", "84.008563 | \n", "33.037907 | \n", "37.280443 | \n", "8.400856 | \n", "3.303791 | \n", "3.728044 | \n", "LP | \n", "18 TH Glut | \n", "connected | \n", "
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9473 rows × 10 columns
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