{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 3_ctx_th_connection_and_gene_correlation" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import scanpy as sc\n", "from tqdm import tqdm\n", "import matplotlib.pyplot as plt\n", "import anndata as ad\n", "import numpy as np\n", "import warnings\n", "from scipy.stats import pearsonr\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", "\n", "warnings.filterwarnings('ignore')\n" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "(107909, 107909)\n" ] }, { "data": { "text/plain": [ "AnnData object with n_obs × n_vars = 107909 × 1122\n", " obs: 'x', 'y', 'z', 'section', 'NT_index', 'Cells_id', 'region', 'spot_num'\n", " uns: 'log1p'" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "adj = np.load('/mnt/Data18Td/Data/haichao/mouse_connect_data/NT/zxw/mouse_3/zxw_not_symmetric_adj.npy', mmap_mode='r')\n", "print(adj.shape)\n", "\n", "adata = sc.read_h5ad('/mnt/Data16Tc/home/haichao/code/SpaCon/ST_NT_cluster/SpaCon_apply_zxw/data/mouse_3/adata_merge.h5ad')\n", "sc.pp.normalize_total(adata, target_sum=1e4)\n", "sc.pp.log1p(adata)\n", "allen_region = pd.read_csv('/mnt/Data16Tc/home/haichao/code/SpaCon/ST_NT_cluster/SpaCon_apply_zxw/data/mouse_3/allen_region.csv')\n", "adata.obs['region'] = allen_region['region'].to_list()\n", "adata.obs['spot_num'] = [i for i in range(adata.n_obs)]\n", "adata" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "### subregion th ctx correlation" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | x | \n", "y | \n", "z | \n", "section | \n", "NT_index | \n", "Cells_id | \n", "region | \n", "spot_num | \n", "CT_spot_num | \n", "ctx_or_th | \n", "
|---|---|---|---|---|---|---|---|---|---|---|
| 2 | \n", "19.113418 | \n", "23.994053 | \n", "46.894548 | \n", "Zhuang-ABCA-3.005 | \n", "2 | \n", "188949490498702611647640449216501815503_304478... | \n", "FRP1 | \n", "0 | \n", "0 | \n", "ctx | \n", "
| 4 | \n", "18.921382 | \n", "24.017347 | \n", "49.257099 | \n", "Zhuang-ABCA-3.004 | \n", "4 | \n", "123445075025856302518661678660778224944_131347... | \n", "FRP1 | \n", "1 | \n", "1 | \n", "ctx | \n", "
| 6 | \n", "19.079053 | \n", "23.564575 | \n", "51.258567 | \n", "Zhuang-ABCA-3.003 | \n", "6 | \n", "319072152716142889780926524544977408256_106358... | \n", "FRP1 | \n", "2 | \n", "2 | \n", "ctx | \n", "
| 7 | \n", "18.816739 | \n", "25.041919 | \n", "43.046671 | \n", "Zhuang-ABCA-3.007 | \n", "7 | \n", "47102176527243727968506801819481818675_1792889... | \n", "FRP1 | \n", "3 | \n", "3 | \n", "ctx | \n", "
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| 148993 | \n", "97.188915 | \n", "11.409533 | \n", "46.662115 | \n", "Zhuang-ABCA-3.005 | \n", "148993 | \n", "107188929587695452503950023602364017291_167314... | \n", "RSPd1 | \n", "75616 | \n", "33098 | \n", "ctx | \n", "
| 193053 | \n", "104.490816 | \n", "24.420635 | \n", "25.679869 | \n", "Zhuang-ABCA-3.015 | \n", "193053 | \n", "43354620289828560228522986006306173486 | \n", "VISpl1 | \n", "99924 | \n", "33099 | \n", "ctx | \n", "
33100 rows × 10 columns
\n", "| \n", " | x | \n", "y | \n", "z | \n", "section | \n", "NT_index | \n", "Cells_id | \n", "region | \n", "spot_num | \n", "CT_spot_num | \n", "ctx_or_th | \n", "subregion | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | \n", "19.113418 | \n", "23.994053 | \n", "46.894548 | \n", "Zhuang-ABCA-3.005 | \n", "2 | \n", "188949490498702611647640449216501815503_304478... | \n", "FRP1 | \n", "0 | \n", "0 | \n", "ctx | \n", "FRP1_2 | \n", "
| 4 | \n", "18.921382 | \n", "24.017347 | \n", "49.257099 | \n", "Zhuang-ABCA-3.004 | \n", "4 | \n", "123445075025856302518661678660778224944_131347... | \n", "FRP1 | \n", "1 | \n", "1 | \n", "ctx | \n", "FRP1_1 | \n", "
| 6 | \n", "19.079053 | \n", "23.564575 | \n", "51.258567 | \n", "Zhuang-ABCA-3.003 | \n", "6 | \n", "319072152716142889780926524544977408256_106358... | \n", "FRP1 | \n", "2 | \n", "2 | \n", "ctx | \n", "FRP1_1 | \n", "
| 7 | \n", "18.816739 | \n", "25.041919 | \n", "43.046671 | \n", "Zhuang-ABCA-3.007 | \n", "7 | \n", "47102176527243727968506801819481818675_1792889... | \n", "FRP1 | \n", "3 | \n", "3 | \n", "ctx | \n", "FRP1_2 | \n", "
| 9 | \n", "18.792692 | \n", "25.077860 | \n", "45.101231 | \n", "Zhuang-ABCA-3.006 | \n", "9 | \n", "199428730039264634225478952930502449426_202483... | \n", "FRP1 | \n", "4 | \n", "4 | \n", "ctx | \n", "FRP1_2 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 148907 | \n", "94.906133 | \n", "15.937666 | \n", "42.404653 | \n", "Zhuang-ABCA-3.007 | \n", "148907 | \n", "106526352840576802488939912804342681931_107003... | \n", "RSPd1 | \n", "75568 | \n", "33095 | \n", "ctx | \n", "RSPd1_3 | \n", "
| 148919 | \n", "95.201531 | \n", "17.993761 | \n", "40.377543 | \n", "Zhuang-ABCA-3.008 | \n", "148919 | \n", "133921573428284040813862276100319739380_145548... | \n", "RSPd1 | \n", "75574 | \n", "33096 | \n", "ctx | \n", "RSPd1_3 | \n", "
| 148971 | \n", "96.095220 | \n", "15.844123 | \n", "42.457680 | \n", "Zhuang-ABCA-3.007 | \n", "148971 | \n", "149021058656557956290496348449572943108_174675... | \n", "RSPd1 | \n", "75604 | \n", "33097 | \n", "ctx | \n", "RSPd1_3 | \n", "
| 148993 | \n", "97.188915 | \n", "11.409533 | \n", "46.662115 | \n", "Zhuang-ABCA-3.005 | \n", "148993 | \n", "107188929587695452503950023602364017291_167314... | \n", "RSPd1 | \n", "75616 | \n", "33098 | \n", "ctx | \n", "RSPd1_2 | \n", "
| 193053 | \n", "104.490816 | \n", "24.420635 | \n", "25.679869 | \n", "Zhuang-ABCA-3.015 | \n", "193053 | \n", "43354620289828560228522986006306173486 | \n", "VISpl1 | \n", "99924 | \n", "33099 | \n", "ctx | \n", "VISpl1_2 | \n", "
33100 rows × 11 columns
\n", "| \n", " | AD_1 | \n", "AMd_1 | \n", "AMd_2 | \n", "AMv_1 | \n", "AV_1 | \n", "AV_2 | \n", "AV_3 | \n", "AV_4 | \n", "AV_5 | \n", "CL_1 | \n", "... | \n", "VPM_23 | \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", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ACAd1_1 | \n", "0.596044 | \n", "0.629380 | \n", "0.629344 | \n", "0.640548 | \n", "0.625990 | \n", "0.616779 | \n", "0.625027 | \n", "0.579291 | \n", "0.607824 | \n", "0.661248 | \n", "... | \n", "0.546631 | \n", "0.580518 | \n", "0.560330 | \n", "0.552390 | \n", "0.588024 | \n", "0.567292 | \n", "0.550110 | \n", "0.595391 | \n", "0.673908 | \n", "0.651029 | \n", "
| ACAd2/3_1 | \n", "0.597459 | \n", "0.627501 | \n", "0.638063 | \n", "0.645888 | \n", "0.624184 | \n", "0.613061 | \n", "0.610360 | \n", "0.584868 | \n", "0.599027 | \n", "0.632073 | \n", "... | \n", "0.563330 | \n", "0.591786 | \n", "0.587295 | \n", "0.583098 | \n", "0.590525 | \n", "0.565894 | \n", "0.574953 | \n", "0.613022 | \n", "0.647487 | \n", "0.650415 | \n", "
| ACAd2/3_2 | \n", "0.571027 | \n", "0.595831 | \n", "0.606491 | \n", "0.613162 | \n", "0.593237 | \n", "0.584572 | \n", "0.577454 | \n", "0.553500 | \n", "0.566546 | \n", "0.593970 | \n", "... | \n", "0.539473 | \n", "0.565224 | \n", "0.567445 | \n", "0.557278 | \n", "0.561655 | \n", "0.535150 | \n", "0.554062 | \n", "0.588653 | \n", "0.610546 | \n", "0.617166 | \n", "
| ACAd2/3_3 | \n", "0.553607 | \n", "0.575565 | \n", "0.594226 | \n", "0.598235 | \n", "0.573342 | \n", "0.568132 | \n", "0.569627 | \n", "0.543022 | \n", "0.554639 | \n", "0.581051 | \n", "... | \n", "0.514714 | \n", "0.539524 | \n", "0.537075 | \n", "0.534365 | \n", "0.534878 | \n", "0.514530 | \n", "0.527182 | \n", "0.561045 | \n", "0.591705 | \n", "0.611740 | \n", "
| ACAd5_1 | \n", "0.630058 | \n", "0.641793 | \n", "0.647781 | \n", "0.654390 | \n", "0.634837 | \n", "0.628741 | \n", "0.631047 | \n", "0.606152 | \n", "0.623477 | \n", "0.657897 | \n", "... | \n", "0.572636 | \n", "0.597883 | \n", "0.591053 | \n", "0.575654 | \n", "0.597200 | \n", "0.584400 | \n", "0.576911 | \n", "0.614796 | \n", "0.669636 | \n", "0.661564 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| VISrl4_1 | \n", "0.608806 | \n", "0.629851 | \n", "0.637136 | \n", "0.650792 | \n", "0.617430 | \n", "0.627219 | \n", "0.614035 | \n", "0.611263 | \n", "0.604888 | \n", "0.627469 | \n", "... | \n", "0.577205 | \n", "0.623548 | \n", "0.610158 | \n", "0.606235 | \n", "0.613583 | \n", "0.559556 | \n", "0.614110 | \n", "0.639994 | \n", "0.649961 | \n", "0.646791 | \n", "
| VISrl5_1 | \n", "0.649082 | \n", "0.647604 | \n", "0.668424 | \n", "0.675256 | \n", "0.653244 | \n", "0.647948 | \n", "0.637781 | \n", "0.631115 | \n", "0.636032 | \n", "0.648355 | \n", "... | \n", "0.617031 | \n", "0.645198 | \n", "0.637634 | \n", "0.624230 | \n", "0.644994 | \n", "0.610415 | \n", "0.630391 | \n", "0.650415 | \n", "0.684320 | \n", "0.669412 | \n", "
| VISrl5_2 | \n", "0.643372 | \n", "0.636174 | \n", "0.654321 | \n", "0.670814 | \n", "0.631363 | \n", "0.641428 | \n", "0.625480 | \n", "0.634172 | \n", "0.618452 | \n", "0.648326 | \n", "... | \n", "0.587593 | \n", "0.635670 | \n", "0.617376 | \n", "0.604309 | \n", "0.627833 | \n", "0.580243 | \n", "0.623062 | \n", "0.645508 | \n", "0.675442 | \n", "0.656189 | \n", "
| VISrl6a_1 | \n", "0.587644 | \n", "0.558709 | \n", "0.591176 | \n", "0.606841 | \n", "0.577877 | \n", "0.581434 | \n", "0.567537 | \n", "0.566168 | \n", "0.559256 | \n", "0.581017 | \n", "... | \n", "0.536177 | \n", "0.560639 | \n", "0.547816 | \n", "0.527045 | \n", "0.555997 | \n", "0.526904 | \n", "0.540306 | \n", "0.558628 | \n", "0.609119 | \n", "0.590757 | \n", "
| VISrl6b_1 | \n", "0.657098 | \n", "0.647202 | \n", "0.689478 | \n", "0.700880 | \n", "0.679191 | \n", "0.673361 | \n", "0.654070 | \n", "0.618012 | \n", "0.638369 | \n", "0.687741 | \n", "... | \n", "0.614595 | \n", "0.632637 | \n", "0.627957 | \n", "0.580900 | \n", "0.653153 | \n", "0.615239 | \n", "0.588846 | \n", "0.612918 | \n", "0.721750 | \n", "0.671169 | \n", "
1475 rows × 244 columns
\n", "