{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 4_ctx_layer56_and_th_correlation" ] }, { "cell_type": "code", "execution_count": 1, "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", "import seaborn as sns\n", "from scipy.cluster.hierarchy import fcluster, linkage\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": [ "
| \n", " | brain_section_label | \n", "x | \n", "y | \n", "z | \n", "x_ccf | \n", "y_ccf | \n", "z_ccf | \n", "region | \n", "cell_type | \n", "
|---|---|---|---|---|---|---|---|---|---|
| cell_label | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| 198904341065180396762707397604803217407 | \n", "Zhuang-ABCA-3.023 | \n", "49.206853 | \n", "44.877634 | \n", "12.168155 | \n", "4.920685 | \n", "4.487763 | \n", "1.216815 | \n", "SSs1 | \n", "33 Vascular | \n", "
| 252199681526991424029643077826220097990 | \n", "Zhuang-ABCA-3.023 | \n", "48.973992 | \n", "44.813761 | \n", "12.179006 | \n", "4.897399 | \n", "4.481376 | \n", "1.217901 | \n", "SSs1 | \n", "33 Vascular | \n", "
| 277720971126854564514249564750701518375 | \n", "Zhuang-ABCA-3.023 | \n", "48.791066 | \n", "44.577722 | \n", "12.192707 | \n", "4.879107 | \n", "4.457772 | \n", "1.219271 | \n", "SSs1 | \n", "33 Vascular | \n", "
| 31551867344111790264292067056219852271 | \n", "Zhuang-ABCA-3.023 | \n", "48.830489 | \n", "44.426120 | \n", "12.195078 | \n", "4.883049 | \n", "4.442612 | \n", "1.219508 | \n", "SSs1 | \n", "33 Vascular | \n", "
| 131102494428104399865219008178262036485 | \n", "Zhuang-ABCA-3.023 | \n", "48.308843 | \n", "43.028156 | \n", "12.267879 | \n", "4.830884 | \n", "4.302816 | \n", "1.226788 | \n", "SSs1 | \n", "34 Immune | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 318102106429791409781741726367984532777 | \n", "Zhuang-ABCA-3.009 | \n", "131.090716 | \n", "69.334275 | \n", "41.436743 | \n", "13.109072 | \n", "6.933427 | \n", "4.143674 | \n", "MDRNd | \n", "30 Astro-Epen | \n", "
| 35262847161560382172299767067854387528 | \n", "Zhuang-ABCA-3.009 | \n", "131.216032 | \n", "69.494070 | \n", "41.351034 | \n", "13.121603 | \n", "6.949407 | \n", "4.135103 | \n", "MDRNd | \n", "33 Vascular | \n", "
| 75415866509570969932943497000463821106 | \n", "Zhuang-ABCA-3.009 | \n", "131.415152 | \n", "70.764504 | \n", "40.800403 | \n", "13.141515 | \n", "7.076450 | \n", "4.080040 | \n", "sctd | \n", "24 MY Glut | \n", "
| 12350978322417280063239916106423065862 | \n", "Zhuang-ABCA-3.009 | \n", "131.646167 | \n", "71.182557 | \n", "40.595995 | \n", "13.164617 | \n", "7.118256 | \n", "4.059599 | \n", "sctd | \n", "24 MY Glut | \n", "
| 327554758863546024460748891922509519354 | \n", "Zhuang-ABCA-3.009 | \n", "131.658892 | \n", "71.414675 | \n", "40.501356 | \n", "13.165889 | \n", "7.141468 | \n", "4.050136 | \n", "sctd | \n", "24 MY Glut | \n", "
1566842 rows × 9 columns
\n", "| \n", " | brain_section_label | \n", "x | \n", "y | \n", "z | \n", "x_ccf | \n", "y_ccf | \n", "z_ccf | \n", "region | \n", "cell_type | \n", "
|---|---|---|---|---|---|---|---|---|---|
| cell_label | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| 29162871883387929795006067736640436040 | \n", "Zhuang-ABCA-3.023 | \n", "61.666898 | \n", "42.255912 | \n", "12.232613 | \n", "6.166690 | \n", "4.225591 | \n", "1.223261 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 293032136699589827732370249746624703959 | \n", "Zhuang-ABCA-3.023 | \n", "62.396840 | \n", "41.838307 | \n", "12.216430 | \n", "6.239684 | \n", "4.183831 | \n", "1.221643 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 169008133492981499504077797165914124518 | \n", "Zhuang-ABCA-3.023 | \n", "64.994841 | \n", "40.394608 | \n", "12.161029 | \n", "6.499484 | \n", "4.039461 | \n", "1.216103 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 227494694293280194589855295428860091482 | \n", "Zhuang-ABCA-3.023 | \n", "64.498586 | \n", "40.611089 | \n", "12.175537 | \n", "6.449859 | \n", "4.061109 | \n", "1.217554 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 33873656525375865261837620890496116573 | \n", "Zhuang-ABCA-3.023 | \n", "64.282103 | \n", "41.059249 | \n", "12.175800 | \n", "6.428210 | \n", "4.105925 | \n", "1.217580 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 229580843941555951333299912014571135110 | \n", "Zhuang-ABCA-3.009 | \n", "97.429638 | \n", "10.575478 | \n", "38.381706 | \n", "9.742964 | \n", "1.057548 | \n", "3.838171 | \n", "VISp5 | \n", "01 IT-ET Glut | \n", "
| 248292745152448671917314233790662445907 | \n", "Zhuang-ABCA-3.009 | \n", "97.150793 | \n", "11.549455 | \n", "38.284627 | \n", "9.715079 | \n", "1.154945 | \n", "3.828463 | \n", "VISp5 | \n", "01 IT-ET Glut | \n", "
| 329636896424947842904418891891676096227 | \n", "Zhuang-ABCA-3.009 | \n", "97.098822 | \n", "10.816952 | \n", "38.350628 | \n", "9.709882 | \n", "1.081695 | \n", "3.835063 | \n", "VISp5 | \n", "01 IT-ET Glut | \n", "
| 210578552686403511812793479380810073674 | \n", "Zhuang-ABCA-3.009 | \n", "98.298868 | \n", "11.674211 | \n", "38.311367 | \n", "9.829887 | \n", "1.167421 | \n", "3.831137 | \n", "VISp5 | \n", "01 IT-ET Glut | \n", "
| 5967642066674772504918301827478668961 | \n", "Zhuang-ABCA-3.009 | \n", "98.354235 | \n", "12.399570 | \n", "38.259130 | \n", "9.835423 | \n", "1.239957 | \n", "3.825913 | \n", "VISp5 | \n", "01 IT-ET Glut | \n", "
60861 rows × 9 columns
\n", "| \n", " | brain_section_label | \n", "x | \n", "y | \n", "z | \n", "x_ccf | \n", "y_ccf | \n", "z_ccf | \n", "region | \n", "cell_type | \n", "
|---|---|---|---|---|---|---|---|---|---|
| cell_label | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| 29162871883387929795006067736640436040 | \n", "Zhuang-ABCA-3.023 | \n", "61.666898 | \n", "42.255912 | \n", "12.232613 | \n", "6.166690 | \n", "4.225591 | \n", "1.223261 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 293032136699589827732370249746624703959 | \n", "Zhuang-ABCA-3.023 | \n", "62.396840 | \n", "41.838307 | \n", "12.216430 | \n", "6.239684 | \n", "4.183831 | \n", "1.221643 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 169008133492981499504077797165914124518 | \n", "Zhuang-ABCA-3.023 | \n", "64.994841 | \n", "40.394608 | \n", "12.161029 | \n", "6.499484 | \n", "4.039461 | \n", "1.216103 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 227494694293280194589855295428860091482 | \n", "Zhuang-ABCA-3.023 | \n", "64.498586 | \n", "40.611089 | \n", "12.175537 | \n", "6.449859 | \n", "4.061109 | \n", "1.217554 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "
| 33873656525375865261837620890496116573 | \n", "Zhuang-ABCA-3.023 | \n", "64.282103 | \n", "41.059249 | \n", "12.175800 | \n", "6.428210 | \n", "4.105925 | \n", "1.217580 | \n", "SSs5 | \n", "01 IT-ET Glut | \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", "
| 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", "
| 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", "
| 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", "
| 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", "
71462 rows × 9 columns
\n", "| \n", " | brain_section_label | \n", "x | \n", "y | \n", "z | \n", "x_ccf | \n", "y_ccf | \n", "z_ccf | \n", "region | \n", "cell_type | \n", "subregion | \n", "
|---|---|---|---|---|---|---|---|---|---|---|
| cell_label | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| 29162871883387929795006067736640436040 | \n", "Zhuang-ABCA-3.023 | \n", "61.666898 | \n", "42.255912 | \n", "12.232613 | \n", "6.166690 | \n", "4.225591 | \n", "1.223261 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "SSs5_16 | \n", "
| 293032136699589827732370249746624703959 | \n", "Zhuang-ABCA-3.023 | \n", "62.396840 | \n", "41.838307 | \n", "12.216430 | \n", "6.239684 | \n", "4.183831 | \n", "1.221643 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "SSs5_16 | \n", "
| 169008133492981499504077797165914124518 | \n", "Zhuang-ABCA-3.023 | \n", "64.994841 | \n", "40.394608 | \n", "12.161029 | \n", "6.499484 | \n", "4.039461 | \n", "1.216103 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "SSs5_15 | \n", "
| 227494694293280194589855295428860091482 | \n", "Zhuang-ABCA-3.023 | \n", "64.498586 | \n", "40.611089 | \n", "12.175537 | \n", "6.449859 | \n", "4.061109 | \n", "1.217554 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "SSs5_15 | \n", "
| 33873656525375865261837620890496116573 | \n", "Zhuang-ABCA-3.023 | \n", "64.282103 | \n", "41.059249 | \n", "12.175800 | \n", "6.428210 | \n", "4.105925 | \n", "1.217580 | \n", "SSs5 | \n", "01 IT-ET Glut | \n", "SSs5_15 | \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", "SGN_1 | \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", "POL_1 | \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", "SGN_1 | \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", "POL_1 | \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", "POL_1 | \n", "
71462 rows × 10 columns
\n", "| \n", " | AD_1 | \n", "AD_2 | \n", "AD_3 | \n", "AV_1 | \n", "AV_2 | \n", "AV_3 | \n", "AV_4 | \n", "CL_1 | \n", "CL_2 | \n", "CM_1 | \n", "... | \n", "VPM_2 | \n", "VPM_3 | \n", "VPM_4 | \n", "VPM_5 | \n", "VPM_6 | \n", "VPM_7 | \n", "VPM_8 | \n", "VPM_9 | \n", "VPMpc_1 | \n", "VPMpc_2 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ACAd5_1 | \n", "0.410782 | \n", "0.399958 | \n", "0.429878 | \n", "0.389128 | \n", "0.399872 | \n", "0.379626 | \n", "0.385972 | \n", "0.433726 | \n", "0.448486 | \n", "0.418421 | \n", "... | \n", "0.349622 | \n", "0.392964 | \n", "0.367910 | \n", "0.383102 | \n", "0.396261 | \n", "0.393593 | \n", "0.400477 | \n", "0.395913 | \n", "0.471805 | \n", "0.461550 | \n", "
| ACAd5_10 | \n", "0.393125 | \n", "0.382621 | \n", "0.415251 | \n", "0.376264 | \n", "0.384030 | \n", "0.365063 | \n", "0.373579 | \n", "0.424826 | \n", "0.446542 | \n", "0.411051 | \n", "... | \n", "0.326493 | \n", "0.371632 | \n", "0.347403 | \n", "0.361314 | \n", "0.376664 | \n", "0.377090 | \n", "0.379626 | \n", "0.376344 | \n", "0.458214 | \n", "0.458316 | \n", "
| ACAd5_11 | \n", "0.398234 | \n", "0.380920 | \n", "0.420792 | \n", "0.413818 | \n", "0.409845 | \n", "0.394324 | \n", "0.400633 | \n", "0.455472 | \n", "0.467039 | \n", "0.445792 | \n", "... | \n", "0.374350 | \n", "0.416192 | \n", "0.391017 | \n", "0.403894 | \n", "0.426616 | \n", "0.423503 | \n", "0.427803 | \n", "0.423335 | \n", "0.489865 | \n", "0.486841 | \n", "
| ACAd5_12 | \n", "0.410527 | \n", "0.393434 | \n", "0.435584 | \n", "0.420335 | \n", "0.419085 | \n", "0.401034 | \n", "0.407594 | \n", "0.460431 | \n", "0.469367 | \n", "0.445620 | \n", "... | \n", "0.388494 | \n", "0.428909 | \n", "0.405853 | \n", "0.419587 | \n", "0.437670 | \n", "0.435193 | \n", "0.440099 | \n", "0.432376 | \n", "0.496598 | \n", "0.487125 | \n", "
| ACAd5_13 | \n", "0.396818 | \n", "0.378964 | \n", "0.416866 | \n", "0.407649 | \n", "0.404479 | \n", "0.390833 | \n", "0.399343 | \n", "0.460673 | \n", "0.475524 | \n", "0.454787 | \n", "... | \n", "0.371024 | \n", "0.411906 | \n", "0.387836 | \n", "0.398777 | \n", "0.426981 | \n", "0.425960 | \n", "0.424657 | \n", "0.425608 | \n", "0.492338 | \n", "0.495915 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| VISrl5_3 | \n", "0.403946 | \n", "0.392158 | \n", "0.447694 | \n", "0.412068 | \n", "0.431390 | \n", "0.391572 | \n", "0.398629 | \n", "0.458871 | \n", "0.478694 | \n", "0.423189 | \n", "... | \n", "0.357283 | \n", "0.430841 | \n", "0.399325 | \n", "0.415467 | \n", "0.413560 | \n", "0.410179 | \n", "0.426174 | \n", "0.418796 | \n", "0.503235 | \n", "0.475361 | \n", "
| VISrl6a_1 | \n", "0.353894 | \n", "0.351150 | \n", "0.377903 | \n", "0.321932 | \n", "0.336051 | \n", "0.315114 | \n", "0.315966 | \n", "0.350315 | \n", "0.362867 | \n", "0.331669 | \n", "... | \n", "0.279148 | \n", "0.314711 | \n", "0.289657 | \n", "0.306511 | \n", "0.303450 | \n", "0.303453 | \n", "0.311159 | \n", "0.308828 | \n", "0.377244 | \n", "0.372180 | \n", "
| VISrl6a_2 | \n", "0.329470 | \n", "0.328920 | \n", "0.359324 | \n", "0.318948 | \n", "0.331033 | \n", "0.303589 | \n", "0.304252 | \n", "0.347650 | \n", "0.365771 | \n", "0.318220 | \n", "... | \n", "0.264400 | \n", "0.316115 | \n", "0.284581 | \n", "0.302115 | \n", "0.291393 | \n", "0.287109 | \n", "0.301932 | \n", "0.298410 | \n", "0.378667 | \n", "0.372998 | \n", "
| VISrl6a_3 | \n", "0.350070 | \n", "0.348513 | \n", "0.380515 | \n", "0.334510 | \n", "0.347604 | \n", "0.322965 | \n", "0.320802 | \n", "0.363974 | \n", "0.382227 | \n", "0.333347 | \n", "... | \n", "0.267162 | \n", "0.328005 | \n", "0.294717 | \n", "0.311189 | \n", "0.304804 | \n", "0.300980 | \n", "0.316639 | \n", "0.313798 | \n", "0.396515 | \n", "0.383178 | \n", "
| VISrl6b_1 | \n", "0.322910 | \n", "0.323277 | \n", "0.349623 | \n", "0.307613 | \n", "0.317701 | \n", "0.302240 | \n", "0.302237 | \n", "0.339289 | \n", "0.357366 | \n", "0.312219 | \n", "... | \n", "0.243223 | \n", "0.289870 | \n", "0.263871 | \n", "0.276627 | \n", "0.276174 | \n", "0.275492 | \n", "0.282320 | \n", "0.282552 | \n", "0.361067 | \n", "0.364670 | \n", "
743 rows × 124 columns
\n", "