{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 9_ctx_3region_DEGs_expression_in_cc" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/mnt/Data16Tc/home/haichao/anaconda3/envs/SpaCon_test/lib/python3.8/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", " from .autonotebook import tqdm as notebook_tqdm\n" ] } ], "source": [ "import pandas as pd\n", "import scanpy as sc\n", "from scipy.spatial import cKDTree\n", "from tqdm import tqdm\n", "import matplotlib.pyplot as plt\n", "\n", "import warnings\n", "import seaborn as sns\n", "import matplotlib as mpl\n", "mpl.rcParams['pdf.fonttype'] = 42\n", "mpl.rcParams['ps.fonttype'] = 42\n", "\n", "warnings.filterwarnings('ignore')" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "### gene exp data" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | totalRNA | \n", "brain_section_label | \n", "x | \n", "y | \n", "z | \n", "n_genes_by_counts | \n", "total_counts | \n", "region | \n", "
|---|---|---|---|---|---|---|---|---|
| 100008170567769574864159172860058606533 | \n", "175 | \n", "Zhuang-ABCA-3.001 | \n", "19.063883 | \n", "33.423346 | \n", "54.106801 | \n", "100 | \n", "175 | \n", "MOB | \n", "
| 100019036144713180485707288452329906643 | \n", "373 | \n", "Zhuang-ABCA-3.001 | \n", "44.290637 | \n", "63.872748 | \n", "53.902462 | \n", "189 | \n", "373 | \n", "NDB | \n", "
| 10002377904544842423531242460024745973 | \n", "277 | \n", "Zhuang-ABCA-3.001 | \n", "63.860525 | \n", "7.998013 | \n", "54.043841 | \n", "126 | \n", "277 | \n", "RSPd2/3 | \n", "
| 100027648052649525810014127621472143070 | \n", "435 | \n", "Zhuang-ABCA-3.001 | \n", "113.480480 | \n", "41.056674 | \n", "54.349928 | \n", "165 | \n", "435 | \n", "arb | \n", "
| 100029875144524072265954931895494067096 | \n", "60 | \n", "Zhuang-ABCA-3.001 | \n", "11.572676 | \n", "37.921554 | \n", "54.370336 | \n", "39 | \n", "60 | \n", "MOB | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 99961718914838042706216314325649765172 | \n", "627 | \n", "Zhuang-ABCA-3.001 | \n", "113.199100 | \n", "23.661374 | \n", "54.096322 | \n", "157 | \n", "627 | \n", "CENT3 | \n", "
| 9996242280180655885872867452807576494 | \n", "157 | \n", "Zhuang-ABCA-3.001 | \n", "86.896566 | \n", "18.326938 | \n", "54.027272 | \n", "100 | \n", "157 | \n", "SCop | \n", "
| 999921392501518309214993564089572563 | \n", "97 | \n", "Zhuang-ABCA-3.001 | \n", "21.082878 | \n", "31.635078 | \n", "54.090905 | \n", "67 | \n", "97 | \n", "ORBm1 | \n", "
| 99995909784199304193294645747252265238 | \n", "154 | \n", "Zhuang-ABCA-3.001 | \n", "111.605478 | \n", "22.417974 | \n", "54.070819 | \n", "93 | \n", "154 | \n", "CENT3 | \n", "
| 99996568769251334694329666788053033728 | \n", "200 | \n", "Zhuang-ABCA-3.001 | \n", "112.945756 | \n", "31.433985 | \n", "54.093405 | \n", "95 | \n", "200 | \n", "CENT3 | \n", "
83602 rows × 8 columns
\n", "| \n", " | gene | \n", "score | \n", "logfoldchanges | \n", "pvals | \n", "pvals_adj | \n", "
|---|---|---|---|---|---|
| region | \n", "\n", " | \n", " | \n", " | \n", " | \n", " |
| ctx3 | \n", "Nr2f2 | \n", "10.998008 | \n", "2.251740 | \n", "3.906658e-28 | \n", "2.346106e-27 | \n", "
| ctx3 | \n", "Tshz2 | \n", "42.789413 | \n", "1.908488 | \n", "0.000000e+00 | \n", "0.000000e+00 | \n", "
| ctx3 | \n", "Met | \n", "15.654150 | \n", "1.551293 | \n", "3.112418e-55 | \n", "2.659920e-54 | \n", "
| ctx3 | \n", "Ctxn3 | \n", "5.829773 | \n", "1.497417 | \n", "5.550263e-09 | \n", "1.995580e-08 | \n", "
| ctx3 | \n", "C1ql2 | \n", "4.970668 | \n", "1.410147 | \n", "6.672248e-07 | \n", "2.193156e-06 | \n", "
| ctx2 | \n", "Scn4b | \n", "33.871655 | \n", "1.264914 | \n", "1.742216e-251 | \n", "6.452006e-249 | \n", "
| ctx2 | \n", "Bmpr1b | \n", "13.590011 | \n", "1.168321 | \n", "4.590144e-42 | \n", "8.792501e-41 | \n", "
| ctx2 | \n", "Adgrl2 | \n", "57.814980 | \n", "1.156904 | \n", "0.000000e+00 | \n", "0.000000e+00 | \n", "
| ctx2 | \n", "Blnk | \n", "15.697517 | \n", "1.049282 | \n", "1.572777e-55 | \n", "5.139282e-54 | \n", "
| ctx2 | \n", "Plekha2 | \n", "13.359410 | \n", "1.018079 | \n", "1.043885e-40 | \n", "1.840883e-39 | \n", "
| ctx1 | \n", "Crym | \n", "70.281998 | \n", "3.123753 | \n", "0.000000e+00 | \n", "0.000000e+00 | \n", "
| ctx1 | \n", "Col6a1 | \n", "49.039230 | \n", "2.726512 | \n", "0.000000e+00 | \n", "0.000000e+00 | \n", "
| ctx1 | \n", "Col12a1 | \n", "45.270657 | \n", "2.506889 | \n", "0.000000e+00 | \n", "0.000000e+00 | \n", "
| ctx1 | \n", "Tnfrsf8 | \n", "15.637980 | \n", "2.191909 | \n", "4.012542e-55 | \n", "3.277893e-54 | \n", "
| ctx1 | \n", "Prss12 | \n", "57.639507 | \n", "2.105650 | \n", "0.000000e+00 | \n", "0.000000e+00 | \n", "