qPCR-analysis-220606-plate1to3.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "ec1f6d73-3ad7-4908-89d5-2f7ca6735fbf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mkdir: ../jupyter_figures: File exists\n"
     ]
    }
   ],
   "source": [
    "import sys, os, glob, warnings, logging\n",
    "import string\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib\n",
    "import matplotlib.pyplot as plt\n",
    "import seaborn as sns\n",
    "from scipy import stats\n",
    "from sw_plotting import change_bar_width\n",
    "from sw_utilities import tukeyTest\n",
    "\n",
    "logging.basicConfig(stream=sys.stdout, format='%(asctime)s - %(levelname)s - %(message)s', level=logging.ERROR)\n",
    "# logging.basicConfig(stream=sys.stdout, format='%(asctime)s - %(levelname)s - %(message)s', level=logging.INFO)\n",
    "# logging.basicConfig(stream=sys.stdout, format='%(asctime)s - %(levelname)s - %(message)s', level=logging.DEBUG)\n",
    "\n",
    "# ignore warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "\n",
    "# plotting configuration\n",
    "font = {'family' : 'Arial',\n",
    "        'size'   : 7}\n",
    "matplotlib.rc('font', **font)\n",
    "plt.rcParams['svg.fonttype'] = 'none'\n",
    "\n",
    "# Make a folder if it is not already there to store exported figures\n",
    "!mkdir ../jupyter_figures\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "f561ed82-2192-4426-8adf-df14b0d35732",
   "metadata": {},
   "outputs": [],
   "source": [
    "def layout_to_annotation(plate_id,\n",
    "                         data_folder='../data/qPCR-data',\n",
    "                         template_layout_file=None,\n",
    "                         primer_layout_file=None):\n",
    "    '''\n",
    "    '''\n",
    "    if template_layout_file is None:\n",
    "        template_layout_files = glob.glob(os.path.join(data_folder, '*'+plate_id+'*template*layout*.csv'))\n",
    "        assert len(template_layout_files) == 1\n",
    "        template_layout_file = template_layout_files[0]\n",
    "    \n",
    "    if primer_layout_file is None:\n",
    "        primer_layout_files = glob.glob(os.path.join(data_folder, '*'+plate_id+'*primer*layout*.csv'))\n",
    "        assert len(primer_layout_files) == 1\n",
    "        primer_layout_file = primer_layout_files[0]\n",
    "    \n",
    "    # Extract template information\n",
    "    with open(template_layout_file, 'r') as f:\n",
    "        lines = f.readlines()\n",
    "    assert lines[0].startswith('template')\n",
    "    \n",
    "    template_list = []\n",
    "    for line in lines[1:]:\n",
    "        temp = line.strip().split(',')\n",
    "        assert len(temp) == 13\n",
    "        template_list = template_list + temp[1:]\n",
    "\n",
    "    assert len(template_list) == 96\n",
    "    \n",
    "    # Extract primer information\n",
    "    with open(primer_layout_file, 'r') as f:\n",
    "        lines = f.readlines()\n",
    "    assert lines[0].startswith('primer')\n",
    "    \n",
    "    primer_list = []\n",
    "    for line in lines[1:]:\n",
    "        temp = line.strip().split(',')\n",
    "        assert len(temp) == 13\n",
    "        primer_list = primer_list + temp[1:]\n",
    "\n",
    "    assert len(primer_list) == 96\n",
    "    \n",
    "    wells = []\n",
    "    for i in string.ascii_uppercase[:8]:\n",
    "        for j in range(1,13):\n",
    "            wells.append(i+'{:02d}'.format(j))\n",
    "    \n",
    "    annotation_file = os.path.join(data_folder, plate_id+'-annotation.csv')\n",
    "    with open(annotation_file, 'w') as f:\n",
    "        f.write(','.join(['Well', 'Sample', 'Primer']) + '\\n')\n",
    "        for i in range(96):\n",
    "            f.write(','.join([wells[i], template_list[i], primer_list[i]]) + '\\n')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "29cf1fd1-af0b-460f-ab20-94cf83041b6e",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_plate_data(plate_id, data_folder='../data/qPCR-data'):\n",
    "    ''' Given a plate id:\n",
    "          1. Locate the annotation csv file and the quantification Cq results csv file\n",
    "          2. Extract useful data, merge and return the data frame\n",
    "    '''\n",
    "    layout_to_annotation(plate_id)\n",
    "    annotation_files = glob.glob(os.path.join(data_folder, '*'+plate_id+'*annotation.csv'))\n",
    "    assert len(annotation_files) == 1\n",
    "    annotation_file = annotation_files[0]\n",
    "    \n",
    "    exported_csv_folders = glob.glob(os.path.join(data_folder, '*'+plate_id+'*'+os.path.sep))\n",
    "    assert len(exported_csv_folders) == 1\n",
    "    exported_csv_folder = exported_csv_folders[0]\n",
    "    \n",
    "    data_files = glob.glob(os.path.join(exported_csv_folder, '*Quantification Cq Results.csv'))\n",
    "    assert len(data_files) == 1\n",
    "    data_file = data_files[0]\n",
    "    \n",
    "    df = pd.read_csv(annotation_file)\n",
    "    df_annotation = df[['Well', 'Sample', 'Primer']]\n",
    "    \n",
    "    df = pd.read_csv(data_file)\n",
    "    df_data = df[['Well', 'Cq']]\n",
    "    \n",
    "    df = df_annotation.merge(df_data, on='Well')\n",
    "    df.dropna(inplace=True)\n",
    "    \n",
    "    return df\n",
    "\n",
    "def get_expression_data(df, test_primer, ref_primer='Rps29 v1'):\n",
    "    ''' From the data frame containing qPCR data and annotation, \n",
    "        calculate average values of replicates and deltaCq values of each sample\n",
    "        \n",
    "    '''\n",
    "    for i in ['Well', 'Sample', 'Primer', 'Cq']:\n",
    "        assert i in df.columns\n",
    "    \n",
    "    df_ref = df[df.Primer==ref_primer]\n",
    "    df_ref.rename(columns={'Cq': 'Cq_ref'}, inplace=True)\n",
    "    \n",
    "    df_test = df[df.Primer==test_primer]\n",
    "    df_test.rename(columns={'Cq': 'Cq_test'}, inplace=True)\n",
    "    \n",
    "    # calculate average values of technical replicates\n",
    "    df_ref_mean = df_ref.groupby('Sample').mean()\n",
    "    df_ref_mean.reset_index(inplace=True)\n",
    "    \n",
    "    df_test_mean = df_test.groupby('Sample').mean()\n",
    "    df_test_mean.reset_index(inplace=True)\n",
    "    \n",
    "    df = df_ref_mean.merge(df_test_mean, on='Sample')\n",
    "    df['deltaCq'] = df.Cq_test - df.Cq_ref\n",
    "    df['relExp'] = 2**(-df.deltaCq)\n",
    "    df['Group'] = [df.Sample[i][:-2] for i in range(len(df))]\n",
    "    \n",
    "    return df\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "efcf0422-23ad-4b71-b55b-26a6719ed5a0",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read in data\n",
    "df_plate1 = get_plate_data('220606-plate1')\n",
    "df_plate2 = get_plate_data('220606-plate2')\n",
    "df_plate3 = get_plate_data('220606-plate3')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4a33278c-da84-40cb-aec5-68f7e58deaa7",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Concatenate the data (stacking up and down)\n",
    "df = pd.concat([df_plate1, df_plate2, df_plate3])\n",
    "df.reset_index(inplace=True, drop=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f9906e3e-cd0e-4837-aba8-23a2c5d37064",
   "metadata": {},
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Well</th>\n",
       "      <th>Sample</th>\n",
       "      <th>Primer</th>\n",
       "      <th>Cq</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A01</td>\n",
       "      <td>B-188-1</td>\n",
       "      <td>Rps29 v1</td>\n",
       "      <td>22.184486</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A02</td>\n",
       "      <td>B-188-1</td>\n",
       "      <td>Rps29 v1</td>\n",
       "      <td>22.106597</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>A03</td>\n",
       "      <td>B-188-1</td>\n",
       "      <td>Rps29 v1</td>\n",
       "      <td>21.971934</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>A04</td>\n",
       "      <td>B-317-1</td>\n",
       "      <td>Rps29 v1</td>\n",
       "      <td>21.709593</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>A05</td>\n",
       "      <td>B-317-1</td>\n",
       "      <td>Rps29 v1</td>\n",
       "      <td>21.603098</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>175</th>\n",
       "      <td>E08</td>\n",
       "      <td>B-318-5</td>\n",
       "      <td>Itga6 v1</td>\n",
       "      <td>23.346960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>176</th>\n",
       "      <td>E09</td>\n",
       "      <td>B-318-5</td>\n",
       "      <td>Itga6 v1</td>\n",
       "      <td>23.280773</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>177</th>\n",
       "      <td>E10</td>\n",
       "      <td>B-319-5</td>\n",
       "      <td>Itga6 v1</td>\n",
       "      <td>24.645805</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>178</th>\n",
       "      <td>E11</td>\n",
       "      <td>B-319-5</td>\n",
       "      <td>Itga6 v1</td>\n",
       "      <td>24.777007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>179</th>\n",
       "      <td>E12</td>\n",
       "      <td>B-319-5</td>\n",
       "      <td>Itga6 v1</td>\n",
       "      <td>25.104728</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>180 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    Well   Sample    Primer         Cq\n",
       "0    A01  B-188-1  Rps29 v1  22.184486\n",
       "1    A02  B-188-1  Rps29 v1  22.106597\n",
       "2    A03  B-188-1  Rps29 v1  21.971934\n",
       "3    A04  B-317-1  Rps29 v1  21.709593\n",
       "4    A05  B-317-1  Rps29 v1  21.603098\n",
       "..   ...      ...       ...        ...\n",
       "175  E08  B-318-5  Itga6 v1  23.346960\n",
       "176  E09  B-318-5  Itga6 v1  23.280773\n",
       "177  E10  B-319-5  Itga6 v1  24.645805\n",
       "178  E11  B-319-5  Itga6 v1  24.777007\n",
       "179  E12  B-319-5  Itga6 v1  25.104728\n",
       "\n",
       "[180 rows x 4 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c4c82282-37d7-48e3-870c-7a0f420f172f",
   "metadata": {},
   "outputs": [],
   "source": [
    "df_gene1 = get_expression_data(df, 'Itga3 v1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "697fd19e-be65-4465-847c-fe2eed124674",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "        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>Sample</th>\n",
       "      <th>Cq_ref</th>\n",
       "      <th>Cq_test</th>\n",
       "      <th>deltaCq</th>\n",
       "      <th>relExp</th>\n",
       "      <th>Group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>B-188-1</td>\n",
       "      <td>22.087673</td>\n",
       "      <td>30.137308</td>\n",
       "      <td>8.049635</td>\n",
       "      <td>0.003774</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>B-188-2</td>\n",
       "      <td>19.502547</td>\n",
       "      <td>27.625948</td>\n",
       "      <td>8.123401</td>\n",
       "      <td>0.003586</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>B-188-3</td>\n",
       "      <td>19.237502</td>\n",
       "      <td>27.281748</td>\n",
       "      <td>8.044246</td>\n",
       "      <td>0.003788</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>B-188-4</td>\n",
       "      <td>20.644886</td>\n",
       "      <td>28.047761</td>\n",
       "      <td>7.402875</td>\n",
       "      <td>0.005909</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>B-188-5</td>\n",
       "      <td>20.187498</td>\n",
       "      <td>28.664508</td>\n",
       "      <td>8.477010</td>\n",
       "      <td>0.002807</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>B-317-1</td>\n",
       "      <td>21.692524</td>\n",
       "      <td>30.323398</td>\n",
       "      <td>8.630873</td>\n",
       "      <td>0.002523</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>B-317-2</td>\n",
       "      <td>19.257319</td>\n",
       "      <td>27.571321</td>\n",
       "      <td>8.314002</td>\n",
       "      <td>0.003142</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>B-317-3</td>\n",
       "      <td>20.303602</td>\n",
       "      <td>27.154888</td>\n",
       "      <td>6.851287</td>\n",
       "      <td>0.008661</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>B-317-4</td>\n",
       "      <td>19.985657</td>\n",
       "      <td>27.066783</td>\n",
       "      <td>7.081126</td>\n",
       "      <td>0.007385</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>B-317-5</td>\n",
       "      <td>19.577181</td>\n",
       "      <td>27.225710</td>\n",
       "      <td>7.648529</td>\n",
       "      <td>0.004984</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>B-318-1</td>\n",
       "      <td>22.078745</td>\n",
       "      <td>28.490861</td>\n",
       "      <td>6.412116</td>\n",
       "      <td>0.011743</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>B-318-2</td>\n",
       "      <td>20.426622</td>\n",
       "      <td>28.009014</td>\n",
       "      <td>7.582392</td>\n",
       "      <td>0.005218</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>B-318-3</td>\n",
       "      <td>20.342614</td>\n",
       "      <td>28.915579</td>\n",
       "      <td>8.572965</td>\n",
       "      <td>0.002626</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>B-318-4</td>\n",
       "      <td>19.296662</td>\n",
       "      <td>26.963107</td>\n",
       "      <td>7.666445</td>\n",
       "      <td>0.004922</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>B-318-5</td>\n",
       "      <td>19.953024</td>\n",
       "      <td>27.882403</td>\n",
       "      <td>7.929379</td>\n",
       "      <td>0.004102</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>B-319-1</td>\n",
       "      <td>19.042437</td>\n",
       "      <td>26.237129</td>\n",
       "      <td>7.194692</td>\n",
       "      <td>0.006826</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>B-319-2</td>\n",
       "      <td>18.927449</td>\n",
       "      <td>27.164557</td>\n",
       "      <td>8.237108</td>\n",
       "      <td>0.003314</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>B-319-3</td>\n",
       "      <td>19.864018</td>\n",
       "      <td>26.994277</td>\n",
       "      <td>7.130259</td>\n",
       "      <td>0.007138</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>B-319-4</td>\n",
       "      <td>21.112034</td>\n",
       "      <td>29.590359</td>\n",
       "      <td>8.478325</td>\n",
       "      <td>0.002804</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>B-319-5</td>\n",
       "      <td>20.277085</td>\n",
       "      <td>29.346568</td>\n",
       "      <td>9.069484</td>\n",
       "      <td>0.001861</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     Sample     Cq_ref    Cq_test   deltaCq    relExp  Group\n",
       "0   B-188-1  22.087673  30.137308  8.049635  0.003774  B-188\n",
       "1   B-188-2  19.502547  27.625948  8.123401  0.003586  B-188\n",
       "2   B-188-3  19.237502  27.281748  8.044246  0.003788  B-188\n",
       "3   B-188-4  20.644886  28.047761  7.402875  0.005909  B-188\n",
       "4   B-188-5  20.187498  28.664508  8.477010  0.002807  B-188\n",
       "5   B-317-1  21.692524  30.323398  8.630873  0.002523  B-317\n",
       "6   B-317-2  19.257319  27.571321  8.314002  0.003142  B-317\n",
       "7   B-317-3  20.303602  27.154888  6.851287  0.008661  B-317\n",
       "8   B-317-4  19.985657  27.066783  7.081126  0.007385  B-317\n",
       "9   B-317-5  19.577181  27.225710  7.648529  0.004984  B-317\n",
       "10  B-318-1  22.078745  28.490861  6.412116  0.011743  B-318\n",
       "11  B-318-2  20.426622  28.009014  7.582392  0.005218  B-318\n",
       "12  B-318-3  20.342614  28.915579  8.572965  0.002626  B-318\n",
       "13  B-318-4  19.296662  26.963107  7.666445  0.004922  B-318\n",
       "14  B-318-5  19.953024  27.882403  7.929379  0.004102  B-318\n",
       "15  B-319-1  19.042437  26.237129  7.194692  0.006826  B-319\n",
       "16  B-319-2  18.927449  27.164557  8.237108  0.003314  B-319\n",
       "17  B-319-3  19.864018  26.994277  7.130259  0.007138  B-319\n",
       "18  B-319-4  21.112034  29.590359  8.478325  0.002804  B-319\n",
       "19  B-319-5  20.277085  29.346568  9.069484  0.001861  B-319"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_gene1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "4b470502-bb83-4815-97e9-a9dd204d42ef",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AxesSubplot:xlabel='Group', ylabel='relExp'>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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mXA18DDgVEV8AXke13HNJRHyWKvx/o8t1SwvyDF+pQyLibzJzvuUgqecMf0kqkGv+klQgw1+SCmT4S1KBDH9JKpDhL0kF+n9cI/rGRxNZpwAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "sns.barplot(data=df_gene1, x='Group', y='relExp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "b96876ad-46e2-446c-8b58-5947c1b37e2e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AxesSubplot:xlabel='Group', ylabel='relExp'>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "sns.scatterplot(data=df_gene1, x='Group', y='relExp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "b6c69dab-e451-4279-9b6f-bf2f39fc6943",
   "metadata": {},
   "outputs": [],
   "source": [
    "df_gene2 = get_expression_data(df, 'Itga6 v1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "2be6a5c6-2e38-43d4-860e-c0236f6253de",
   "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>Sample</th>\n",
       "      <th>Cq_ref</th>\n",
       "      <th>Cq_test</th>\n",
       "      <th>deltaCq</th>\n",
       "      <th>relExp</th>\n",
       "      <th>Group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>B-188-1</td>\n",
       "      <td>22.087673</td>\n",
       "      <td>26.108284</td>\n",
       "      <td>4.020612</td>\n",
       "      <td>0.061613</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>B-188-2</td>\n",
       "      <td>19.502547</td>\n",
       "      <td>23.701103</td>\n",
       "      <td>4.198556</td>\n",
       "      <td>0.054464</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>B-188-3</td>\n",
       "      <td>19.237502</td>\n",
       "      <td>23.107661</td>\n",
       "      <td>3.870159</td>\n",
       "      <td>0.068386</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>B-188-4</td>\n",
       "      <td>20.644886</td>\n",
       "      <td>24.297625</td>\n",
       "      <td>3.652739</td>\n",
       "      <td>0.079509</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>B-188-5</td>\n",
       "      <td>20.187498</td>\n",
       "      <td>24.187729</td>\n",
       "      <td>4.000231</td>\n",
       "      <td>0.062490</td>\n",
       "      <td>B-188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>B-317-1</td>\n",
       "      <td>21.692524</td>\n",
       "      <td>25.875536</td>\n",
       "      <td>4.183012</td>\n",
       "      <td>0.055054</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>B-317-2</td>\n",
       "      <td>19.257319</td>\n",
       "      <td>23.298045</td>\n",
       "      <td>4.040726</td>\n",
       "      <td>0.060760</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>B-317-3</td>\n",
       "      <td>20.303602</td>\n",
       "      <td>23.629349</td>\n",
       "      <td>3.325748</td>\n",
       "      <td>0.099736</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>B-317-4</td>\n",
       "      <td>19.985657</td>\n",
       "      <td>23.381478</td>\n",
       "      <td>3.395822</td>\n",
       "      <td>0.095007</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>B-317-5</td>\n",
       "      <td>19.577181</td>\n",
       "      <td>23.139124</td>\n",
       "      <td>3.561943</td>\n",
       "      <td>0.084674</td>\n",
       "      <td>B-317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>B-318-1</td>\n",
       "      <td>22.078745</td>\n",
       "      <td>25.064629</td>\n",
       "      <td>2.985884</td>\n",
       "      <td>0.126229</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>B-318-2</td>\n",
       "      <td>20.426622</td>\n",
       "      <td>23.774679</td>\n",
       "      <td>3.348057</td>\n",
       "      <td>0.098205</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>B-318-3</td>\n",
       "      <td>20.342614</td>\n",
       "      <td>24.219779</td>\n",
       "      <td>3.877164</td>\n",
       "      <td>0.068055</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>B-318-4</td>\n",
       "      <td>19.296662</td>\n",
       "      <td>22.808727</td>\n",
       "      <td>3.512066</td>\n",
       "      <td>0.087652</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>B-318-5</td>\n",
       "      <td>19.953024</td>\n",
       "      <td>23.419036</td>\n",
       "      <td>3.466012</td>\n",
       "      <td>0.090495</td>\n",
       "      <td>B-318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>B-319-1</td>\n",
       "      <td>19.042437</td>\n",
       "      <td>22.725829</td>\n",
       "      <td>3.683393</td>\n",
       "      <td>0.077837</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>B-319-2</td>\n",
       "      <td>18.927449</td>\n",
       "      <td>23.092171</td>\n",
       "      <td>4.164722</td>\n",
       "      <td>0.055756</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>B-319-3</td>\n",
       "      <td>19.864018</td>\n",
       "      <td>23.305787</td>\n",
       "      <td>3.441769</td>\n",
       "      <td>0.092029</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>B-319-4</td>\n",
       "      <td>21.112034</td>\n",
       "      <td>25.271030</td>\n",
       "      <td>4.158996</td>\n",
       "      <td>0.055978</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>B-319-5</td>\n",
       "      <td>20.277085</td>\n",
       "      <td>24.842513</td>\n",
       "      <td>4.565429</td>\n",
       "      <td>0.042235</td>\n",
       "      <td>B-319</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     Sample     Cq_ref    Cq_test   deltaCq    relExp  Group\n",
       "0   B-188-1  22.087673  26.108284  4.020612  0.061613  B-188\n",
       "1   B-188-2  19.502547  23.701103  4.198556  0.054464  B-188\n",
       "2   B-188-3  19.237502  23.107661  3.870159  0.068386  B-188\n",
       "3   B-188-4  20.644886  24.297625  3.652739  0.079509  B-188\n",
       "4   B-188-5  20.187498  24.187729  4.000231  0.062490  B-188\n",
       "5   B-317-1  21.692524  25.875536  4.183012  0.055054  B-317\n",
       "6   B-317-2  19.257319  23.298045  4.040726  0.060760  B-317\n",
       "7   B-317-3  20.303602  23.629349  3.325748  0.099736  B-317\n",
       "8   B-317-4  19.985657  23.381478  3.395822  0.095007  B-317\n",
       "9   B-317-5  19.577181  23.139124  3.561943  0.084674  B-317\n",
       "10  B-318-1  22.078745  25.064629  2.985884  0.126229  B-318\n",
       "11  B-318-2  20.426622  23.774679  3.348057  0.098205  B-318\n",
       "12  B-318-3  20.342614  24.219779  3.877164  0.068055  B-318\n",
       "13  B-318-4  19.296662  22.808727  3.512066  0.087652  B-318\n",
       "14  B-318-5  19.953024  23.419036  3.466012  0.090495  B-318\n",
       "15  B-319-1  19.042437  22.725829  3.683393  0.077837  B-319\n",
       "16  B-319-2  18.927449  23.092171  4.164722  0.055756  B-319\n",
       "17  B-319-3  19.864018  23.305787  3.441769  0.092029  B-319\n",
       "18  B-319-4  21.112034  25.271030  4.158996  0.055978  B-319\n",
       "19  B-319-5  20.277085  24.842513  4.565429  0.042235  B-319"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_gene2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "67053bf4-dc70-423b-beab-9025898c0df9",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AxesSubplot:xlabel='Group', ylabel='relExp'>"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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9JBVg7CWpAGMvSQUYe0kq4P8ATwHmaGOur04AAAAASUVORK5CYII=\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "sns.barplot(data=df_gene2, x='Group', y='relExp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "9c68a898-c7f6-47ab-9684-32ff9fc44529",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AxesSubplot:xlabel='Group', ylabel='relExp'>"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "sns.scatterplot(data=df_gene2, x='Group', y='relExp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "2bffe1f3-3923-42eb-a02b-bac1ab9501dc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Summary of test:\n",
      " Multiple Comparison of Means - Tukey HSD, FWER=0.05\n",
      "===================================================\n",
      "group1 group2 meandiff p-adj   lower  upper  reject\n",
      "---------------------------------------------------\n",
      " B-188  B-317   0.0014  0.819 -0.0033  0.006  False\n",
      " B-188  B-318   0.0017 0.6923 -0.0029 0.0064  False\n",
      " B-188  B-319   0.0004    0.9 -0.0042 0.0051  False\n",
      " B-317  B-318   0.0004    0.9 -0.0043  0.005  False\n",
      " B-317  B-319   -0.001    0.9 -0.0056 0.0037  False\n",
      " B-318  B-319  -0.0013 0.8298  -0.006 0.0033  False\n",
      "---------------------------------------------------\n",
      "p values of all pair-wise tests:\n",
      " [0.8189667  0.69230943 0.9        0.9        0.9        0.82980493]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<statsmodels.sandbox.stats.multicomp.TukeyHSDResults at 0x7ff321e96340>"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tukeyTest(df_gene1.relExp, df_gene1.Group)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "0bb6b0af-aa55-40bf-b4b7-d89955511833",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Summary of test:\n",
      " Multiple Comparison of Means - Tukey HSD, FWER=0.05\n",
      "===================================================\n",
      "group1 group2 meandiff p-adj   lower  upper  reject\n",
      "---------------------------------------------------\n",
      " B-188  B-317   0.0138 0.6288 -0.0193 0.0468  False\n",
      " B-188  B-318   0.0288 0.0987 -0.0042 0.0619  False\n",
      " B-188  B-319  -0.0005    0.9 -0.0336 0.0325  False\n",
      " B-317  B-318   0.0151 0.5669  -0.018 0.0481  False\n",
      " B-317  B-319  -0.0143 0.6043 -0.0473 0.0188  False\n",
      " B-318  B-319  -0.0294 0.0909 -0.0624 0.0037  False\n",
      "---------------------------------------------------\n",
      "p values of all pair-wise tests:\n",
      " [0.6288147  0.09870922 0.9        0.56687211 0.60429918 0.09085507]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<statsmodels.sandbox.stats.multicomp.TukeyHSDResults at 0x7ff321e963d0>"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tukeyTest(df_gene2.relExp, df_gene2.Group)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "18fb20db-5b7c-4b80-a381-f4d53d78e263",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
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   "language": "python",
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