685 lines
37 KiB
Plaintext
685 lines
37 KiB
Plaintext
|
{
|
||
|
|
"cells": [
|
||
|
|
{
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"id": "6f6aa857",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"# Exercise: Compute summary statistics for the neural data"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 1,
|
||
|
|
"id": "8f9bc8b1",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": [
|
||
|
|
"%matplotlib inline\n",
|
||
|
|
"\n",
|
||
|
|
"import matplotlib.pyplot as plt\n",
|
||
|
|
"import pandas as pd\n",
|
||
|
|
"\n",
|
||
|
|
"# Set some Pandas options: maximum number of rows/columns it's going to display\n",
|
||
|
|
"pd.set_option('display.max_rows', 1000)\n",
|
||
|
|
"pd.set_option('display.max_columns', 100)"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"id": "1be11d54",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"# Load the processed neural data"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 2,
|
||
|
|
"id": "d2dfebd3",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": [
|
||
|
|
"df = pd.read_csv('processed_QC_passed_2024-07-04_collected_v1.csv')"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 3,
|
||
|
|
"id": "09554c84",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [
|
||
|
|
{
|
||
|
|
"data": {
|
||
|
|
"text/plain": [
|
||
|
|
"(659, 35)"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 3,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"df.shape"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 4,
|
||
|
|
"id": "df95a10b",
|
||
|
|
"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>OP</th>\n",
|
||
|
|
" <th>filename</th>\n",
|
||
|
|
" <th>slice</th>\n",
|
||
|
|
" <th>cell_ch</th>\n",
|
||
|
|
" <th>cell_ID</th>\n",
|
||
|
|
" <th>day</th>\n",
|
||
|
|
" <th>treatment</th>\n",
|
||
|
|
" <th>hrs_incubation</th>\n",
|
||
|
|
" <th>repatch</th>\n",
|
||
|
|
" <th>hrs_after_OP</th>\n",
|
||
|
|
" <th>Rs</th>\n",
|
||
|
|
" <th>Rin</th>\n",
|
||
|
|
" <th>resting_potential</th>\n",
|
||
|
|
" <th>max_spikes</th>\n",
|
||
|
|
" <th>Rheobase</th>\n",
|
||
|
|
" <th>AP_heigth</th>\n",
|
||
|
|
" <th>TH</th>\n",
|
||
|
|
" <th>max_depol</th>\n",
|
||
|
|
" <th>max_repol</th>\n",
|
||
|
|
" <th>membra_time_constant_tau</th>\n",
|
||
|
|
" <th>capacitance</th>\n",
|
||
|
|
" <th>comments</th>\n",
|
||
|
|
" <th>rheo_ramp</th>\n",
|
||
|
|
" <th>AP_halfwidth</th>\n",
|
||
|
|
" <th>Rheobse_ramp</th>\n",
|
||
|
|
" <th>Unnamed: 27</th>\n",
|
||
|
|
" <th>rheos_ramp</th>\n",
|
||
|
|
" <th>comment</th>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" <th>high K concentration</th>\n",
|
||
|
|
" <th>RMP_from_char</th>\n",
|
||
|
|
" <th>tissue_source</th>\n",
|
||
|
|
" <th>area</th>\n",
|
||
|
|
" <th>patient_age</th>\n",
|
||
|
|
" <th>patcher</th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </thead>\n",
|
||
|
|
" <tbody>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>0</th>\n",
|
||
|
|
" <td>OP230420</td>\n",
|
||
|
|
" <td>23420003.abf</td>\n",
|
||
|
|
" <td>S1</td>\n",
|
||
|
|
" <td>1</td>\n",
|
||
|
|
" <td>23420S1c1</td>\n",
|
||
|
|
" <td>D1</td>\n",
|
||
|
|
" <td>TTX</td>\n",
|
||
|
|
" <td>0.0</td>\n",
|
||
|
|
" <td>no</td>\n",
|
||
|
|
" <td>10.416389</td>\n",
|
||
|
|
" <td>6.675643</td>\n",
|
||
|
|
" <td>39.025301</td>\n",
|
||
|
|
" <td>-74.285889</td>\n",
|
||
|
|
" <td>24</td>\n",
|
||
|
|
" <td>200.0</td>\n",
|
||
|
|
" <td>80.749512</td>\n",
|
||
|
|
" <td>-35.278320</td>\n",
|
||
|
|
" <td>336.181641</td>\n",
|
||
|
|
" <td>-60.791016</td>\n",
|
||
|
|
" <td>19.40</td>\n",
|
||
|
|
" <td>510.601767</td>\n",
|
||
|
|
" <td>0</td>\n",
|
||
|
|
" <td>753.380113</td>\n",
|
||
|
|
" <td>1.151009</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>8 mM</td>\n",
|
||
|
|
" <td>-61.828554</td>\n",
|
||
|
|
" <td>Bielefeld</td>\n",
|
||
|
|
" <td>temporal</td>\n",
|
||
|
|
" <td>13.0</td>\n",
|
||
|
|
" <td>Verji</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>1</th>\n",
|
||
|
|
" <td>OP230420</td>\n",
|
||
|
|
" <td>23420003.abf</td>\n",
|
||
|
|
" <td>S1</td>\n",
|
||
|
|
" <td>3</td>\n",
|
||
|
|
" <td>23420S1c3</td>\n",
|
||
|
|
" <td>D1</td>\n",
|
||
|
|
" <td>TTX</td>\n",
|
||
|
|
" <td>0.0</td>\n",
|
||
|
|
" <td>no</td>\n",
|
||
|
|
" <td>10.416389</td>\n",
|
||
|
|
" <td>7.867174</td>\n",
|
||
|
|
" <td>48.728367</td>\n",
|
||
|
|
" <td>-69.573975</td>\n",
|
||
|
|
" <td>26</td>\n",
|
||
|
|
" <td>300.0</td>\n",
|
||
|
|
" <td>78.448486</td>\n",
|
||
|
|
" <td>-32.043457</td>\n",
|
||
|
|
" <td>350.097656</td>\n",
|
||
|
|
" <td>-67.138672</td>\n",
|
||
|
|
" <td>17.30</td>\n",
|
||
|
|
" <td>393.397918</td>\n",
|
||
|
|
" <td>1</td>\n",
|
||
|
|
" <td>585.102837</td>\n",
|
||
|
|
" <td>1.006321</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>8 mM</td>\n",
|
||
|
|
" <td>-60.460298</td>\n",
|
||
|
|
" <td>Bielefeld</td>\n",
|
||
|
|
" <td>temporal</td>\n",
|
||
|
|
" <td>13.0</td>\n",
|
||
|
|
" <td>Verji</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>2</th>\n",
|
||
|
|
" <td>OP230420</td>\n",
|
||
|
|
" <td>23420003.abf</td>\n",
|
||
|
|
" <td>S1</td>\n",
|
||
|
|
" <td>6</td>\n",
|
||
|
|
" <td>23420S1c6</td>\n",
|
||
|
|
" <td>D1</td>\n",
|
||
|
|
" <td>TTX</td>\n",
|
||
|
|
" <td>0.0</td>\n",
|
||
|
|
" <td>no</td>\n",
|
||
|
|
" <td>10.416389</td>\n",
|
||
|
|
" <td>8.820134</td>\n",
|
||
|
|
" <td>35.971082</td>\n",
|
||
|
|
" <td>-54.956055</td>\n",
|
||
|
|
" <td>22</td>\n",
|
||
|
|
" <td>300.0</td>\n",
|
||
|
|
" <td>76.660156</td>\n",
|
||
|
|
" <td>-29.827881</td>\n",
|
||
|
|
" <td>270.629883</td>\n",
|
||
|
|
" <td>-52.246094</td>\n",
|
||
|
|
" <td>14.85</td>\n",
|
||
|
|
" <td>426.098774</td>\n",
|
||
|
|
" <td>3</td>\n",
|
||
|
|
" <td>173.915797</td>\n",
|
||
|
|
" <td>1.266335</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>8 mM</td>\n",
|
||
|
|
" <td>-59.615979</td>\n",
|
||
|
|
" <td>Bielefeld</td>\n",
|
||
|
|
" <td>temporal</td>\n",
|
||
|
|
" <td>13.0</td>\n",
|
||
|
|
" <td>Verji</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>3</th>\n",
|
||
|
|
" <td>OP230420</td>\n",
|
||
|
|
" <td>23420003.abf</td>\n",
|
||
|
|
" <td>S1</td>\n",
|
||
|
|
" <td>8</td>\n",
|
||
|
|
" <td>23420S1c8</td>\n",
|
||
|
|
" <td>D1</td>\n",
|
||
|
|
" <td>TTX</td>\n",
|
||
|
|
" <td>0.0</td>\n",
|
||
|
|
" <td>yes</td>\n",
|
||
|
|
" <td>10.416389</td>\n",
|
||
|
|
" <td>6.000400</td>\n",
|
||
|
|
" <td>31.599917</td>\n",
|
||
|
|
" <td>-70.550537</td>\n",
|
||
|
|
" <td>22</td>\n",
|
||
|
|
" <td>350.0</td>\n",
|
||
|
|
" <td>81.011963</td>\n",
|
||
|
|
" <td>-33.068848</td>\n",
|
||
|
|
" <td>309.448242</td>\n",
|
||
|
|
" <td>-61.401367</td>\n",
|
||
|
|
" <td>16.65</td>\n",
|
||
|
|
" <td>575.513924</td>\n",
|
||
|
|
" <td>5</td>\n",
|
||
|
|
" <td>786.927898</td>\n",
|
||
|
|
" <td>1.182830</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>8 mM</td>\n",
|
||
|
|
" <td>-60.956350</td>\n",
|
||
|
|
" <td>Bielefeld</td>\n",
|
||
|
|
" <td>temporal</td>\n",
|
||
|
|
" <td>13.0</td>\n",
|
||
|
|
" <td>Verji</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>4</th>\n",
|
||
|
|
" <td>OP230420</td>\n",
|
||
|
|
" <td>23420061.abf</td>\n",
|
||
|
|
" <td>S1_D2</td>\n",
|
||
|
|
" <td>8</td>\n",
|
||
|
|
" <td>23420S1c8</td>\n",
|
||
|
|
" <td>D2</td>\n",
|
||
|
|
" <td>TTX</td>\n",
|
||
|
|
" <td>19.0</td>\n",
|
||
|
|
" <td>yes</td>\n",
|
||
|
|
" <td>29.633333</td>\n",
|
||
|
|
" <td>8.271614</td>\n",
|
||
|
|
" <td>30.607259</td>\n",
|
||
|
|
" <td>-70.745850</td>\n",
|
||
|
|
" <td>1</td>\n",
|
||
|
|
" <td>1300.0</td>\n",
|
||
|
|
" <td>48.883057</td>\n",
|
||
|
|
" <td>-20.855713</td>\n",
|
||
|
|
" <td>100.952148</td>\n",
|
||
|
|
" <td>-27.465820</td>\n",
|
||
|
|
" <td>13.25</td>\n",
|
||
|
|
" <td>864.892430</td>\n",
|
||
|
|
" <td>29</td>\n",
|
||
|
|
" <td>565.938865</td>\n",
|
||
|
|
" <td>1.504127</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>8 mM</td>\n",
|
||
|
|
" <td>-61.283967</td>\n",
|
||
|
|
" <td>Bielefeld</td>\n",
|
||
|
|
" <td>temporal</td>\n",
|
||
|
|
" <td>13.0</td>\n",
|
||
|
|
" <td>Verji</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </tbody>\n",
|
||
|
|
"</table>\n",
|
||
|
|
"</div>"
|
||
|
|
],
|
||
|
|
"text/plain": [
|
||
|
|
" OP filename slice cell_ch cell_ID day treatment \\\n",
|
||
|
|
"0 OP230420 23420003.abf S1 1 23420S1c1 D1 TTX \n",
|
||
|
|
"1 OP230420 23420003.abf S1 3 23420S1c3 D1 TTX \n",
|
||
|
|
"2 OP230420 23420003.abf S1 6 23420S1c6 D1 TTX \n",
|
||
|
|
"3 OP230420 23420003.abf S1 8 23420S1c8 D1 TTX \n",
|
||
|
|
"4 OP230420 23420061.abf S1_D2 8 23420S1c8 D2 TTX \n",
|
||
|
|
"\n",
|
||
|
|
" hrs_incubation repatch hrs_after_OP Rs Rin \\\n",
|
||
|
|
"0 0.0 no 10.416389 6.675643 39.025301 \n",
|
||
|
|
"1 0.0 no 10.416389 7.867174 48.728367 \n",
|
||
|
|
"2 0.0 no 10.416389 8.820134 35.971082 \n",
|
||
|
|
"3 0.0 yes 10.416389 6.000400 31.599917 \n",
|
||
|
|
"4 19.0 yes 29.633333 8.271614 30.607259 \n",
|
||
|
|
"\n",
|
||
|
|
" resting_potential max_spikes Rheobase AP_heigth TH max_depol \\\n",
|
||
|
|
"0 -74.285889 24 200.0 80.749512 -35.278320 336.181641 \n",
|
||
|
|
"1 -69.573975 26 300.0 78.448486 -32.043457 350.097656 \n",
|
||
|
|
"2 -54.956055 22 300.0 76.660156 -29.827881 270.629883 \n",
|
||
|
|
"3 -70.550537 22 350.0 81.011963 -33.068848 309.448242 \n",
|
||
|
|
"4 -70.745850 1 1300.0 48.883057 -20.855713 100.952148 \n",
|
||
|
|
"\n",
|
||
|
|
" max_repol membra_time_constant_tau capacitance comments rheo_ramp \\\n",
|
||
|
|
"0 -60.791016 19.40 510.601767 0 753.380113 \n",
|
||
|
|
"1 -67.138672 17.30 393.397918 1 585.102837 \n",
|
||
|
|
"2 -52.246094 14.85 426.098774 3 173.915797 \n",
|
||
|
|
"3 -61.401367 16.65 575.513924 5 786.927898 \n",
|
||
|
|
"4 -27.465820 13.25 864.892430 29 565.938865 \n",
|
||
|
|
"\n",
|
||
|
|
" AP_halfwidth Rheobse_ramp Unnamed: 27 rheos_ramp comment \\\n",
|
||
|
|
"0 1.151009 NaN NaN NaN NaN NaN \n",
|
||
|
|
"1 1.006321 NaN NaN NaN NaN NaN \n",
|
||
|
|
"2 1.266335 NaN NaN NaN NaN NaN \n",
|
||
|
|
"3 1.182830 NaN NaN NaN NaN NaN \n",
|
||
|
|
"4 1.504127 NaN NaN NaN NaN NaN \n",
|
||
|
|
"\n",
|
||
|
|
" high K concentration RMP_from_char tissue_source area patient_age \\\n",
|
||
|
|
"0 8 mM -61.828554 Bielefeld temporal 13.0 \n",
|
||
|
|
"1 8 mM -60.460298 Bielefeld temporal 13.0 \n",
|
||
|
|
"2 8 mM -59.615979 Bielefeld temporal 13.0 \n",
|
||
|
|
"3 8 mM -60.956350 Bielefeld temporal 13.0 \n",
|
||
|
|
"4 8 mM -61.283967 Bielefeld temporal 13.0 \n",
|
||
|
|
"\n",
|
||
|
|
" patcher \n",
|
||
|
|
"0 Verji \n",
|
||
|
|
"1 Verji \n",
|
||
|
|
"2 Verji \n",
|
||
|
|
"3 Verji \n",
|
||
|
|
"4 Verji "
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 4,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"df.head()"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"id": "0b4f6091",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"# 1. Does capacitance change with age?\n",
|
||
|
|
"\n",
|
||
|
|
"* Compute the capacitance by patient age, and plot it\n",
|
||
|
|
"* Does it change with age? (eyeballing is enough)"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 5,
|
||
|
|
"id": "00bb9eb1",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [
|
||
|
|
{
|
||
|
|
"data": {
|
||
|
|
"text/plain": [
|
||
|
|
"<Axes: xlabel='patient_age'>"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 5,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"data": {
|
||
|
|
"image/png": "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
|
||
|
|
"text/plain": [
|
||
|
|
"<Figure size 640x480 with 1 Axes>"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "display_data"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"df.groupby('patient_age')['capacitance'].mean().plot(ls='', marker='.')"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"id": "1940d3fe",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"# 2. Spiking threshold after potassium incubation\n",
|
||
|
|
"\n",
|
||
|
|
"1. Does the spiking threshold (TH) change between Day 1 and Day 2?\n",
|
||
|
|
"2. Does this result depend on the treatment?"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 6,
|
||
|
|
"id": "8175fc1c",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [
|
||
|
|
{
|
||
|
|
"data": {
|
||
|
|
"text/plain": [
|
||
|
|
"day\n",
|
||
|
|
"D1 -37.276805\n",
|
||
|
|
"D2 -33.039838\n",
|
||
|
|
"Name: TH, dtype: float64"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 6,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"df.groupby('day')['TH'].mean()"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 7,
|
||
|
|
"id": "fc34eecb",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": [
|
||
|
|
"th_per_treatment_and_day = df.pivot_table(index='treatment', columns='day', values='TH', aggfunc='mean')"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 8,
|
||
|
|
"id": "05761273",
|
||
|
|
"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>day</th>\n",
|
||
|
|
" <th>D1</th>\n",
|
||
|
|
" <th>D2</th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>treatment</th>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </thead>\n",
|
||
|
|
" <tbody>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>Ctrl</th>\n",
|
||
|
|
" <td>-37.865372</td>\n",
|
||
|
|
" <td>-35.751658</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>TTX</th>\n",
|
||
|
|
" <td>-36.852170</td>\n",
|
||
|
|
" <td>-30.008780</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>high K</th>\n",
|
||
|
|
" <td>-36.926069</td>\n",
|
||
|
|
" <td>-33.162092</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>wash in high K</th>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>-35.791016</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </tbody>\n",
|
||
|
|
"</table>\n",
|
||
|
|
"</div>"
|
||
|
|
],
|
||
|
|
"text/plain": [
|
||
|
|
"day D1 D2\n",
|
||
|
|
"treatment \n",
|
||
|
|
"Ctrl -37.865372 -35.751658\n",
|
||
|
|
"TTX -36.852170 -30.008780\n",
|
||
|
|
"high K -36.926069 -33.162092\n",
|
||
|
|
"wash in high K NaN -35.791016"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 8,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"th_per_treatment_and_day"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 9,
|
||
|
|
"id": "95fabcd9",
|
||
|
|
"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 tr th {\n",
|
||
|
|
" text-align: left;\n",
|
||
|
|
" }\n",
|
||
|
|
"\n",
|
||
|
|
" .dataframe thead tr:last-of-type th {\n",
|
||
|
|
" text-align: right;\n",
|
||
|
|
" }\n",
|
||
|
|
"</style>\n",
|
||
|
|
"<table border=\"1\" class=\"dataframe\">\n",
|
||
|
|
" <thead>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" <th colspan=\"2\" halign=\"left\">mean</th>\n",
|
||
|
|
" <th colspan=\"2\" halign=\"left\">std</th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>day</th>\n",
|
||
|
|
" <th>D1</th>\n",
|
||
|
|
" <th>D2</th>\n",
|
||
|
|
" <th>D1</th>\n",
|
||
|
|
" <th>D2</th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>treatment</th>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" <th></th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </thead>\n",
|
||
|
|
" <tbody>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>Ctrl</th>\n",
|
||
|
|
" <td>-37.865372</td>\n",
|
||
|
|
" <td>-35.751658</td>\n",
|
||
|
|
" <td>4.260140</td>\n",
|
||
|
|
" <td>5.459102</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>TTX</th>\n",
|
||
|
|
" <td>-36.852170</td>\n",
|
||
|
|
" <td>-30.008780</td>\n",
|
||
|
|
" <td>5.406569</td>\n",
|
||
|
|
" <td>6.577182</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>high K</th>\n",
|
||
|
|
" <td>-36.926069</td>\n",
|
||
|
|
" <td>-33.162092</td>\n",
|
||
|
|
" <td>3.966294</td>\n",
|
||
|
|
" <td>4.479648</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th>wash in high K</th>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>-35.791016</td>\n",
|
||
|
|
" <td>NaN</td>\n",
|
||
|
|
" <td>1.009906</td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </tbody>\n",
|
||
|
|
"</table>\n",
|
||
|
|
"</div>"
|
||
|
|
],
|
||
|
|
"text/plain": [
|
||
|
|
" mean std \n",
|
||
|
|
"day D1 D2 D1 D2\n",
|
||
|
|
"treatment \n",
|
||
|
|
"Ctrl -37.865372 -35.751658 4.260140 5.459102\n",
|
||
|
|
"TTX -36.852170 -30.008780 5.406569 6.577182\n",
|
||
|
|
"high K -36.926069 -33.162092 3.966294 4.479648\n",
|
||
|
|
"wash in high K NaN -35.791016 NaN 1.009906"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 9,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"th_per_treatment_and_day = df.pivot_table(index='treatment', columns='day', values='TH', aggfunc=['mean', 'std'])\n",
|
||
|
|
"th_per_treatment_and_day"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": null,
|
||
|
|
"id": "dd5023cd",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": []
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"metadata": {
|
||
|
|
"kernelspec": {
|
||
|
|
"display_name": "Python 3 (ipykernel)",
|
||
|
|
"language": "python",
|
||
|
|
"name": "python3"
|
||
|
|
},
|
||
|
|
"language_info": {
|
||
|
|
"codemirror_mode": {
|
||
|
|
"name": "ipython",
|
||
|
|
"version": 3
|
||
|
|
},
|
||
|
|
"file_extension": ".py",
|
||
|
|
"mimetype": "text/x-python",
|
||
|
|
"name": "python",
|
||
|
|
"nbconvert_exporter": "python",
|
||
|
|
"pygments_lexer": "ipython3",
|
||
|
|
"version": "3.11.3"
|
||
|
|
}
|
||
|
|
},
|
||
|
|
"nbformat": 4,
|
||
|
|
"nbformat_minor": 5
|
||
|
|
}
|