408 lines
14 KiB
Plaintext
408 lines
14 KiB
Plaintext
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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "6f6aa857",
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"metadata": {},
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"source": [
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"# Exercise: For each patcher, compute the average number of days they waited between experiments\n",
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"\n",
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"Here is how to proceed\n",
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"1. Use a window function to compute the number of days that elapse between experiment (i.e., the distance between `date`), for each `patcher`. Add that as a new column, `'days from prev'`\n",
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"2. Compute the average `'days from prev'` per patcher\n",
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"\n",
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"With your new awesome vectorization skills, it should take two lines!"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "8f9bc8b1",
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"metadata": {},
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"outputs": [],
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"source": [
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"import pandas as pd\n",
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"\n",
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"# Set some Pandas options: maximum number of rows/columns it's going to display\n",
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"pd.set_option('display.max_rows', 1000)\n",
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"pd.set_option('display.max_columns', 100)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "1be11d54",
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"metadata": {},
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"source": [
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"# Load the neural data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 61,
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"id": "b6b1abff",
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"metadata": {},
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"outputs": [],
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"source": [
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"df = pd.read_csv('shuffled_QC_passed_2024-07-04_collected_v1.csv', parse_dates=['date'])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 62,
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"id": "c0237922",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<div>\n",
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"<style scoped>\n",
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" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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" }\n",
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"\n",
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" .dataframe tbody tr th {\n",
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" vertical-align: top;\n",
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" }\n",
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"\n",
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" .dataframe thead th {\n",
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" text-align: right;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
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" <th>OP</th>\n",
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" <th>patcher</th>\n",
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" <th>date</th>\n",
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" <th>slice</th>\n",
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" <th>cell_ch</th>\n",
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" <th>cell_ID</th>\n",
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" <th>day</th>\n",
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" <th>treatment</th>\n",
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" <th>hrs_incubation</th>\n",
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" <th>repatch</th>\n",
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" <th>hrs_after_OP</th>\n",
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" <th>Rs</th>\n",
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" <th>Rin</th>\n",
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" <th>resting_potential</th>\n",
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" <th>max_spikes</th>\n",
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" <th>Rheobase</th>\n",
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" <th>AP_heigth</th>\n",
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" <th>TH</th>\n",
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" <th>max_depol</th>\n",
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" <th>max_repol</th>\n",
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" <th>membra_time_constant_tau</th>\n",
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" <th>capacitance</th>\n",
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" <th>comments</th>\n",
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" <th>rheo_ramp</th>\n",
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" <th>AP_halfwidth</th>\n",
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" <th>Rheobse_ramp</th>\n",
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" <th>Unnamed: 27</th>\n",
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" <th>rheos_ramp</th>\n",
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" <th>comment</th>\n",
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" <th></th>\n",
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" <th>high K concentration</th>\n",
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" <th>RMP_from_char</th>\n",
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" <th>tissue_source</th>\n",
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" <th>area</th>\n",
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" <th>patient_age</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
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" <td>OP211209</td>\n",
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" <td>Verji</td>\n",
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" <td>2024-03-13</td>\n",
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" <td>S2</td>\n",
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" <td>8</td>\n",
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" <td>21d10S2c8</td>\n",
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" <td>D1</td>\n",
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" <td>Ctrl</td>\n",
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" <td>0.0</td>\n",
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" <td>no</td>\n",
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" <td>13.298889</td>\n",
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" <td>14.470281</td>\n",
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" <td>166.878916</td>\n",
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" <td>-67.962646</td>\n",
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" <td>34</td>\n",
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" <td>50.0</td>\n",
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" <td>83.190918</td>\n",
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" <td>-36.132812</td>\n",
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" <td>302.124023</td>\n",
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" <td>-72.631836</td>\n",
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" <td>20.75</td>\n",
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" <td>152.623120</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>0.966102</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>15 mM</td>\n",
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" <td>-59.101382</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>27.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>1</th>\n",
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" <td>OP221024</td>\n",
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" <td>Verji</td>\n",
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" <td>2024-06-16</td>\n",
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" <td>S3</td>\n",
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" <td>4</td>\n",
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" <td>22o24S3c4</td>\n",
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" <td>D1</td>\n",
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" <td>Ctrl</td>\n",
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" <td>0.0</td>\n",
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" <td>no</td>\n",
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" <td>23.964167</td>\n",
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" <td>11.521243</td>\n",
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" <td>137.820797</td>\n",
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" <td>-71.789551</td>\n",
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" <td>41</td>\n",
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" <td>50.0</td>\n",
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" <td>93.322754</td>\n",
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" <td>-42.968750</td>\n",
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" <td>465.820312</td>\n",
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" <td>-83.740234</td>\n",
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" <td>14.85</td>\n",
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" <td>124.324170</td>\n",
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" <td>17</td>\n",
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" <td>NaN</td>\n",
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" <td>0.959995</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-62.265689</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>42.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
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" <td>OP230810</td>\n",
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" <td>Verji</td>\n",
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" <td>2024-05-14</td>\n",
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" <td>S2</td>\n",
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" <td>5</td>\n",
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" <td>23810S2c5</td>\n",
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" <td>D1</td>\n",
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" <td>TTX</td>\n",
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" <td>0.0</td>\n",
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" <td>no</td>\n",
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" <td>7.043056</td>\n",
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" <td>10.120637</td>\n",
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" <td>67.739416</td>\n",
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" <td>-70.629883</td>\n",
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" <td>47</td>\n",
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" <td>100.0</td>\n",
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" <td>91.973877</td>\n",
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" <td>-37.817383</td>\n",
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" <td>415.771484</td>\n",
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" <td>-107.666016</td>\n",
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" <td>13.00</td>\n",
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" <td>228.654858</td>\n",
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" <td>10</td>\n",
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" <td>402.013400</td>\n",
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" <td>0.760052</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-61.329228</td>\n",
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" <td>Mitte</td>\n",
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" <td>temporal</td>\n",
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" <td>63.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>OP230209</td>\n",
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" <td>Verji</td>\n",
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" <td>2024-04-27</td>\n",
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" <td>S2_D2</td>\n",
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" <td>3</td>\n",
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" <td>23209S2_D2c3</td>\n",
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" <td>D2</td>\n",
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" <td>high K</td>\n",
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" <td>25.0</td>\n",
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" <td>no</td>\n",
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" <td>21.848333</td>\n",
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" <td>7.745503</td>\n",
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" <td>43.009610</td>\n",
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" <td>-68.371582</td>\n",
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" <td>31</td>\n",
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" <td>500.0</td>\n",
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" <td>67.163086</td>\n",
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" <td>-29.284668</td>\n",
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" <td>212.036133</td>\n",
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" <td>-61.645508</td>\n",
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" <td>11.05</td>\n",
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" <td>215.784505</td>\n",
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" <td>30</td>\n",
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" <td>672.202407</td>\n",
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" <td>0.958735</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-62.577472</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>63.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>OP240321</td>\n",
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" <td>Verji</td>\n",
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" <td>2024-04-11</td>\n",
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" <td>S2</td>\n",
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" <td>4</td>\n",
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" <td>24321S2c4</td>\n",
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" <td>D1</td>\n",
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" <td>Ctrl</td>\n",
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" <td>0.0</td>\n",
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" <td>no</td>\n",
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" <td>11.530278</td>\n",
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" <td>7.632941</td>\n",
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" <td>32.884808</td>\n",
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" <td>-52.453613</td>\n",
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" <td>21</td>\n",
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" <td>200.0</td>\n",
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" <td>84.008789</td>\n",
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" <td>-36.785889</td>\n",
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" <td>403.442383</td>\n",
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" <td>-71.899414</td>\n",
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" <td>14.80</td>\n",
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" <td>695.791105</td>\n",
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" <td>8</td>\n",
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" <td>NaN</td>\n",
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" <td>1.063838</td>\n",
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" <td>324.520817</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-63.149769</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>31.0</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"</div>"
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],
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"text/plain": [
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" OP patcher date slice cell_ch cell_ID day treatment \\\n",
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"0 OP211209 Verji 2024-03-13 S2 8 21d10S2c8 D1 Ctrl \n",
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"1 OP221024 Verji 2024-06-16 S3 4 22o24S3c4 D1 Ctrl \n",
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"2 OP230810 Verji 2024-05-14 S2 5 23810S2c5 D1 TTX \n",
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"3 OP230209 Verji 2024-04-27 S2_D2 3 23209S2_D2c3 D2 high K \n",
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"4 OP240321 Verji 2024-04-11 S2 4 24321S2c4 D1 Ctrl \n",
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"\n",
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" hrs_incubation repatch hrs_after_OP Rs Rin \\\n",
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"0 0.0 no 13.298889 14.470281 166.878916 \n",
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"1 0.0 no 23.964167 11.521243 137.820797 \n",
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"2 0.0 no 7.043056 10.120637 67.739416 \n",
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"3 25.0 no 21.848333 7.745503 43.009610 \n",
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"4 0.0 no 11.530278 7.632941 32.884808 \n",
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"\n",
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" resting_potential max_spikes Rheobase AP_heigth TH max_depol \\\n",
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"0 -67.962646 34 50.0 83.190918 -36.132812 302.124023 \n",
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"1 -71.789551 41 50.0 93.322754 -42.968750 465.820312 \n",
|
||
|
|
"2 -70.629883 47 100.0 91.973877 -37.817383 415.771484 \n",
|
||
|
|
"3 -68.371582 31 500.0 67.163086 -29.284668 212.036133 \n",
|
||
|
|
"4 -52.453613 21 200.0 84.008789 -36.785889 403.442383 \n",
|
||
|
|
"\n",
|
||
|
|
" max_repol membra_time_constant_tau capacitance comments rheo_ramp \\\n",
|
||
|
|
"0 -72.631836 20.75 152.623120 NaN NaN \n",
|
||
|
|
"1 -83.740234 14.85 124.324170 17 NaN \n",
|
||
|
|
"2 -107.666016 13.00 228.654858 10 402.013400 \n",
|
||
|
|
"3 -61.645508 11.05 215.784505 30 672.202407 \n",
|
||
|
|
"4 -71.899414 14.80 695.791105 8 NaN \n",
|
||
|
|
"\n",
|
||
|
|
" AP_halfwidth Rheobse_ramp Unnamed: 27 rheos_ramp comment \\\n",
|
||
|
|
"0 0.966102 NaN NaN NaN NaN NaN \n",
|
||
|
|
"1 0.959995 NaN NaN NaN NaN NaN \n",
|
||
|
|
"2 0.760052 NaN NaN NaN NaN NaN \n",
|
||
|
|
"3 0.958735 NaN NaN NaN NaN NaN \n",
|
||
|
|
"4 1.063838 324.520817 NaN NaN NaN NaN \n",
|
||
|
|
"\n",
|
||
|
|
" high K concentration RMP_from_char tissue_source area patient_age \n",
|
||
|
|
"0 15 mM -59.101382 Bielefeld temporal 27.0 \n",
|
||
|
|
"1 8 mM -62.265689 Bielefeld temporal 42.0 \n",
|
||
|
|
"2 8 mM -61.329228 Mitte temporal 63.0 \n",
|
||
|
|
"3 8 mM -62.577472 Bielefeld temporal 63.0 \n",
|
||
|
|
"4 8 mM -63.149769 Bielefeld temporal 31.0 "
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 62,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"df.head()"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": null,
|
||
|
|
"id": "f7c93d25",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": []
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": null,
|
||
|
|
"id": "ff2c32f0",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": []
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": null,
|
||
|
|
"id": "612215d0",
|
||
|
|
"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
|
||
|
|
}
|