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      "name": "1_partners_270921.ipynb",
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        "8224ba3f"
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      "language": "python",
      "name": "python3"
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  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "251063af"
      },
      "source": [
        "# Explore the Pf6+ dataset"
      ],
      "id": "251063af"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "41ceac01"
      },
      "source": [
        "In this notebook we are going to:\n",
        "1. Describe how to setup your environment to run these notebooks for analysis and exploration\n",
        "1. Show how to directly access the data without the need to download them\n",
        "1. Explore some of the data and metadata available\n",
        "1. Showcase the richness of this dataset\n",
        "\n",
        "Before we dig into the data, we want to recognise that this resource was possible because of enormous team efforts around the world over the last 18 years, encompassing 61 studies in 30 different countries. With over 16,500 samples available, we hope to continue disseminating these unique resources and increase their accessibility, so that they ultimately translate into improvements for public health.\n",
        "\n",
        "If you use this resource please remember to also cite the following papers:\n",
        "- **[Pf6]** [MalariaGEN et al. *An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples* (2021) Wellcome Open Res](https://doi.org/10.12688/wellcomeopenres.16168.2)\n",
        "- **[GenRe-Mekong]** [Jacob, CG et al. *Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination* (2021) eLife](https://doi.org/10.7554/eLife.62997)\n",
        "\n",
        "A massive **thank you** to all the partners and contributors involved:\n",
        "<table>\n",
        "<tr>\n",
        "<th align='center'>Pf6</th>\n",
        "<th align='center'>GenRe-Mekong</th>\n",
        "</tr>\n",
        "<tr>\n",
        "<td>\n",
        "\n",
        "```\n",
        "Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia,\n",
        "Alfred Amambua-Ngwa, Chanaki Amaratunga, \n",
        "Roberto Amato, Lucas Amenga-Etego, \n",
        "Ben Andagalu, Tim J. C. Anderson,\n",
        "Voahangy Andrianaranjaka, Tobias Apinjoh, \n",
        "Cristina Ariani, Elizabeth A Ashley, Sarah Auburn,\n",
        "Gordon A. Awandare, Hampate Ba, Vito Baraka, \n",
        "Alyssa E. Barry, Philip Bejon, Gwladys I. Bertin, \n",
        "Maciej F. Boni, Steffen Borrmann, Teun Bousema, \n",
        "Oralee Branch, Peter C. Bull, George B. J. Busby, \n",
        "Thanat Chookajorn, Kesinee Chotivanich, \n",
        "Antoine Claessens, David Conway, Alister Craig, \n",
        "Umberto D Alessandro, Souleymane Dama, \n",
        "Nicholas PJ Day, Brigitte Denis, Mahamadou Diakite, \n",
        "Abdoulaye Djimdé, Christiane Dolecek, Arjen M Dondorp,\n",
        "Chris Drakeley, Eleanor Drury, Patrick Duffy, \n",
        "Diego F. Echeverry, Thomas G. Egwang, Berhanu Erko,\n",
        "Rick M. Fairhurst, Abdul Faiz, Caterina A. Fanello, \n",
        "Mark M. Fukuda, Dionicia Gamboa, Anita Ghansah, \n",
        "Lemu Golassa, Sonia Goncalves,  William L. Hamilton, \n",
        "G. L. Abby Harrison, Lee Hart, Christa Henrichs, \n",
        "Tran Tinh Hien, Catherine A. Hill, Abraham Hodgson, \n",
        "Christina Hubbart, Mallika Imwong, Deus S. Ishengoma,\n",
        "Scott A. Jackson, Chris G. Jacob, Ben Jeffery, \n",
        "Anna E. Jeffreys, Kimberly J. Johnson, \n",
        "Dushyanth Jyothi, Claire Kamaliddin, Edwin Kamau,\n",
        "Mihir Kekre, Krzysztof Kluczynski, Theerarat Kochakarn, \n",
        "Abibatou Konaté, Dominic P. Kwiatkowski, \n",
        "Myat Phone Kyaw, Pharath Lim, Chanthap Lon,\n",
        "Kovana M. Loua, Oumou Maïga-Ascofaré, Cinzia Malangone, \n",
        "Magnus Manske, Jutta Marfurt, Kevin Marsh, \n",
        "Mayfong Mayxay, Alistair Miles, Olivo Miotto, \n",
        "Victor Mobegi, Olugbenga A. Mokuolu, Jacqui Montgomery, \n",
        "Ivo Mueller, Paul N. Newton, Thuy Nguyen,\n",
        "Thuy-Nhien Nguyen, Harald Noed, François Nosten,\n",
        "Rintis Noviyanti, Alexis Nzila, \n",
        "Lynette I. Ochola-Oyier, Harold Ocholla, \n",
        "Abraham Oduro, Irene Omedo, Marie A. Onyamboko, \n",
        "Jean-Bosco Ouedraogo, Kolapo Oyebola, \n",
        "Richard D. Pearson, Norbert Peshu, \n",
        "Aung Pyae Phyo, Chris V. Plowe, Ric N. Price, \n",
        "Sasithon Pukrittayakamee,\n",
        "Milijaona Randrianarivelojosia, \n",
        "Julian C. Rayner, Pascal Ringwald, Kirk A. Rockett, \n",
        "Katherine Rowlands, Lastenia Ruiz, David Saunders, \n",
        "Alex Shayo, Peter Siba, Victoria J. Simpson, \n",
        "Jim Stalker, Xin-zhuan Su, Colin Sutherland, \n",
        "Shannon Takala-Harrison, Livingstone Tavu, \n",
        "Vandana Thathy, Antoinette Tshefu, Federica Verra, \n",
        "Joseph Vinetz, Thomas E. Wellems, Jason Wendler, \n",
        "Nicholas J. White, Ian Wright, William Yavo, Htut Ye \n",
        "    \n",
        "```\n",
        "\n",
        "</td>\n",
        "<td>\n",
        "\n",
        "```\n",
        "Christopher G Jacob, Nguyen Thuy-Nhien, \n",
        "Mayfong Mayxay, Richard J Maude, \n",
        "Huynh Hong Quang, Bouasy Hongvanthong, \n",
        "Viengxay Vanisaveth, Thang Ngo Duc,\n",
        "Huy Rekol, Rob van der Pluijm, \n",
        "Lorenz von Seidlein,Rick Fairhurst,\n",
        "François Nosten, Md Amir Hossain, \n",
        "Naomi Park, Scott Goodwin, \n",
        "Pascal Ringwald, \n",
        "Keobouphaphone Chindavongsa,\n",
        "Paul Newton, Elizabeth Ashley, \n",
        "Sonexay Phalivong, Rapeephan Maude, \n",
        "Rithea Leang, Cheah Huch, \n",
        "Le Thanh Dong, Kim-Tuyen Nguyen,\n",
        "Tran Minh Nhat, Tran Tinh Hien, \n",
        "Hoa Nguyen, Nicole Zdrojewski, \n",
        "Sara Canavati, Abdullah Abu Sayeed, \n",
        "Didar Uddin, Caroline Buckee, \n",
        "Caterina I Fanello, Marie Onyamboko, \n",
        "Thomas Peto, Rupam Tripura, \n",
        "Chanaki Amaratunga, Aung Myint Thu, \n",
        "Gilles Delmas, Jordi Landier, \n",
        "Daniel M Parker, Nguyen Hoang Chau, \n",
        "Dysoley Lek, Seila Suon, \n",
        "James Callery, Podjanee Jittamala, \n",
        "Borimas Hanboonkunupakarn,\n",
        "Sasithon Pukrittayakamee, \n",
        "Aung Pyae Phyo, Frank Smithuis, \n",
        "Khin Lin, Myo Thant, \n",
        "Tin Maung Hlaing, Parthasarathi Satpathi, \n",
        "Sanghamitra Satpathi, Prativa K Behera, \n",
        "Amar Tripura, Subrata Baidya, \n",
        "Neena Valecha, Anupkumar R Anvikar, \n",
        "Akhter Ul Islam, Abul Faiz, \n",
        "Chanon Kunasol, Eleanor Drury,\n",
        "Mihir Kekre, Mozam Ali,\n",
        "Katie Love, Shavanthi Rajatileka,\n",
        "Anna E Jeffreys, Kate Rowlands, \n",
        "Christina S Hubbart, Mehul Dhorda,\n",
        "Ranitha Vongpromek, Namfon Kotanan,\n",
        "Phrutsamon Wongnak, Jacob Almagro Garcia,\n",
        "Richard D Pearson, Cristina V Ariani,\n",
        "Thanat Chookajorn, Cinzia Malangone,\n",
        "T Nguyen, Jim Stalker,\n",
        "Ben Jeffery, Jonathan Keatley, \n",
        "Kimberly J Johnson, Dawn Muddyman,\n",
        "Xin Hui S Chan, John Sillitoe,\n",
        "Roberto Amato, Victoria Simpson,\n",
        "Sonia Gonçalves, Kirk Rockett,\n",
        "Nicholas P Day, Arjen M Dondorp,\n",
        "Dominic P Kwiatkowski, Olivo Miotto\n",
        "    \n",
        "```\n",
        "\n",
        "</td>\n",
        "</tr>\n",
        "</table>"
      ],
      "id": "41ceac01"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ff2dba27"
      },
      "source": [
        "---"
      ],
      "id": "ff2dba27"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "a20ad1e7"
      },
      "source": [
        "## Pf6+ Resource Exploration"
      ],
      "id": "a20ad1e7"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "80b77306"
      },
      "source": [
        "### Setting up your environment and notebooks \n",
        "\n",
        "There are two ways to access the Pf6+ data resource and analysis notebooks, either: \n",
        "- Run notebooks with a Google Colaboratory environment [Google colab](https://research.google.com/colaboratory/). All you need is a Google account. \n",
        "- Run on a local jupyter instance on your computer."
      ],
      "id": "80b77306"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "4249973a"
      },
      "source": [
        "#### If you are running this on Google Colab\n",
        "If you are running the notebooks on Colab, then run the cell below to clone [the Pf6+ repo](https://github.com/malariagen/Pf6plus):"
      ],
      "id": "4249973a"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "eae5a23c"
      },
      "source": [
        "!git clone https://github.com/malariagen/Pf6plus.git \n",
        "!cp -r /content/Pf6plus/pf6plus_documentation/notebooks/data_analysis ."
      ],
      "id": "eae5a23c",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fcdbf62d"
      },
      "source": [
        "#### If you are running this locally \n",
        "If you prefer to run the notebooks locally, there are additional steps required. If you haven't already, please follow these [instructions](https://github.com/malariagen/Pf6plus#running-the-notebooks-locally) from the Pf6+ repo in Github for more information on local setup."
      ],
      "id": "fcdbf62d"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "bd5a467c"
      },
      "source": [
        "## Get started\n",
        "\n",
        "In order to generate the plots as seen in these notebooks, first import the functions from the `data_analysis` directory, which contain all of the code you will need: "
      ],
      "id": "bd5a467c"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "bd76c886"
      },
      "source": [
        "from data_analysis.map_samples import *\n",
        "from data_analysis.plot_sample_info import *\n",
        "\n",
        "# run to ensure plots show in static page\n",
        "import bokeh.io \n",
        "bokeh.io.output_notebook()"
      ],
      "id": "bd76c886",
      "execution_count": 3,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "bd70b139"
      },
      "source": [
        "## Load the dataset\n",
        "\n",
        "The Pf6+ data resource builds on the efforts of the latest [Pf6](https://wellcomeopenresearch.org/articles/6-42/v1) and the [GenRe-Mekong](https://elifesciences.org/articles/62997) data resources, integrating 7,000 whole-genome sequenced samples together with 10,000 genotyped samples. \n",
        "\n",
        "**Pf6+ is a highly heterogeneous data resource that contains samples from multiple independent studies and technologies (whole-genome sequencing, amplicon sequencing, and Agena genotyping): care needs to be taken when interpreting the aggregated analysis contained in these notebooks and any further work you may do.**\n",
        "\n",
        "### Import the Pf6+ data\n",
        "\n",
        "The command below reads the data directly from the online repository, without needing to download it first. However, you can still decide to download the dataset locally from <a href='https://pf6plus.cog.sanger.ac.uk/pf6plus_metadata.tsv' download='pf6plus_metadata.tsv'>https://pf6plus.cog.sanger.ac.uk/pf6plus_metadata.tsv</a> and modify the line below to point to the correct location."
      ],
      "id": "bd70b139"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "ed2232e6"
      },
      "source": [
        "# URL of the dataset; change accordingly if you prefer to work from a local, offline copy\n",
        "pf6plus_fn = 'https://pf6plus.cog.sanger.ac.uk/pf6plus_metadata.tsv'\n",
        "\n",
        "# Read the dataset\n",
        "pf6plus_all = pd.read_csv(pf6plus_fn, sep='\\t', index_col=0, low_memory=False)"
      ],
      "id": "ed2232e6",
      "execution_count": 4,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "46f11450"
      },
      "source": [
        "## Which information is available to explore?"
      ],
      "id": "46f11450"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "57bf6b1a",
        "outputId": "2a834bd7-4963-4648-a605-21419e69917d",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 488
        }
      },
      "source": [
        "print(pf6plus_all.shape)\n",
        "pf6plus_all.head()"
      ],
      "id": "57bf6b1a",
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "(16720, 166)\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Study</th>\n",
              "      <th>Year</th>\n",
              "      <th>Country</th>\n",
              "      <th>AdmDiv1</th>\n",
              "      <th>Population</th>\n",
              "      <th>Process</th>\n",
              "      <th>IncludeInAnalysis</th>\n",
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              "      <th>Longitude_country</th>\n",
              "      <th>Latitude_adm1</th>\n",
              "      <th>Longitude_adm1</th>\n",
              "      <th>PfCRT</th>\n",
              "      <th>Kelch</th>\n",
              "      <th>PfDHFR</th>\n",
              "      <th>PfEXO</th>\n",
              "      <th>PGB</th>\n",
              "      <th>Plasmepsin2/3</th>\n",
              "      <th>PfDHPS</th>\n",
              "      <th>PfMDR1</th>\n",
              "      <th>Species</th>\n",
              "      <th>Pf3D7_02_v3:376222</th>\n",
              "      <th>Pf3D7_02_v3:470013</th>\n",
              "      <th>Pf3D7_03_v3:656861</th>\n",
              "      <th>Pf3D7_04_v3:110442</th>\n",
              "      <th>Pf3D7_04_v3:881571</th>\n",
              "      <th>Pf3D7_05_v3:350933</th>\n",
              "      <th>Pf3D7_05_v3:369740</th>\n",
              "      <th>Pf3D7_06_v3:900278</th>\n",
              "      <th>Pf3D7_07_v3:1044052</th>\n",
              "      <th>Pf3D7_08_v3:1314831</th>\n",
              "      <th>Pf3D7_08_v3:413067</th>\n",
              "      <th>Pf3D7_09_v3:900277</th>\n",
              "      <th>Pf3D7_11_v3:1018899</th>\n",
              "      <th>Pf3D7_11_v3:1815412</th>\n",
              "      <th>Pf3D7_13_v3:1056452</th>\n",
              "      <th>Pf3D7_13_v3:1466422</th>\n",
              "      <th>Pf3D7_14_v3:137622</th>\n",
              "      <th>Pf3D7_14_v3:2164225</th>\n",
              "      <th>Pf3D7_01_v3:145515</th>\n",
              "      <th>Pf3D7_03_v3:548178</th>\n",
              "      <th>...</th>\n",
              "      <th>Pyrimethamine</th>\n",
              "      <th>Sulfadoxine</th>\n",
              "      <th>S-P</th>\n",
              "      <th>S-P-IPTp</th>\n",
              "      <th>PfCRT:72</th>\n",
              "      <th>PfCRT:74</th>\n",
              "      <th>PfCRT:75</th>\n",
              "      <th>PfCRT:76</th>\n",
              "      <th>PfCRT:93</th>\n",
              "      <th>PfCRT:97</th>\n",
              "      <th>PfCRT:218</th>\n",
              "      <th>PfCRT:220</th>\n",
              "      <th>PfCRT:271</th>\n",
              "      <th>PfCRT:333</th>\n",
              "      <th>PfCRT:353</th>\n",
              "      <th>PfCRT:371</th>\n",
              "      <th>PfDHFR:16</th>\n",
              "      <th>PfDHFR:51</th>\n",
              "      <th>PfDHFR:59</th>\n",
              "      <th>PfDHFR:108</th>\n",
              "      <th>PfDHFR:164</th>\n",
              "      <th>PfDHFR:306</th>\n",
              "      <th>PfDHPS:436</th>\n",
              "      <th>PfDHPS:437</th>\n",
              "      <th>PfDHPS:540</th>\n",
              "      <th>PfDHPS:581</th>\n",
              "      <th>PfDHPS:613</th>\n",
              "      <th>PfEXO:415</th>\n",
              "      <th>PfMDR1:86</th>\n",
              "      <th>PfMDR1:184</th>\n",
              "      <th>PfMDR1:1034</th>\n",
              "      <th>PfMDR1:1042</th>\n",
              "      <th>PfMDR1:1226</th>\n",
              "      <th>PfMDR1:1246</th>\n",
              "      <th>PfARPS10:127</th>\n",
              "      <th>PfARPS10:128</th>\n",
              "      <th>PfFD:193</th>\n",
              "      <th>PfCRT:326</th>\n",
              "      <th>PfCRT:356</th>\n",
              "      <th>PfMDR2:484</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SampleId</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
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              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
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              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
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              "      <th></th>\n",
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              "      <th></th>\n",
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              "      <th></th>\n",
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              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>FP0008-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "      <td>WGS</td>\n",
              "      <td>True</td>\n",
              "      <td>20.265149</td>\n",
              "      <td>-10.337093</td>\n",
              "      <td>16.565426</td>\n",
              "      <td>-9.832345</td>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>ANC[S/N]IS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDN[T/I]DT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-[A/S][A/G]KAA</td>\n",
              "      <td>N[F/Y]D</td>\n",
              "      <td>Pf</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>...</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>[T/K]</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>[S/A]</td>\n",
              "      <td>E</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>[I/R]</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>[S/N]</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>[A/S]</td>\n",
              "      <td>[A/G]</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>[F/Y]</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>N</td>\n",
              "      <td>[T/I]</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0009-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "      <td>WGS</td>\n",
              "      <td>True</td>\n",
              "      <td>20.265149</td>\n",
              "      <td>-10.337093</td>\n",
              "      <td>16.565426</td>\n",
              "      <td>-9.832345</td>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>AIRNIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNTDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-AAKAA</td>\n",
              "      <td>YFY</td>\n",
              "      <td>Pf</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>...</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>E</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>I</td>\n",
              "      <td>A</td>\n",
              "      <td>I</td>\n",
              "      <td>R</td>\n",
              "      <td>N</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>Y</td>\n",
              "      <td>F</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>Y</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0015-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "      <td>WGS</td>\n",
              "      <td>True</td>\n",
              "      <td>20.265149</td>\n",
              "      <td>-10.337093</td>\n",
              "      <td>16.565426</td>\n",
              "      <td>-9.832345</td>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>AIRNIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNIDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-[A/S][A/G]KAA</td>\n",
              "      <td>N[F/Y]D</td>\n",
              "      <td>Pf</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>...</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>E</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>I</td>\n",
              "      <td>A</td>\n",
              "      <td>I</td>\n",
              "      <td>R</td>\n",
              "      <td>N</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>[A/S]</td>\n",
              "      <td>[A/G]</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>[F/Y]</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>N</td>\n",
              "      <td>I</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0016-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "      <td>WGS</td>\n",
              "      <td>True</td>\n",
              "      <td>20.265149</td>\n",
              "      <td>-10.337093</td>\n",
              "      <td>16.565426</td>\n",
              "      <td>-9.832345</td>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>ANCSIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNIDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-SGKAA</td>\n",
              "      <td>NFD</td>\n",
              "      <td>Pf</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>...</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>[T/K]</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>E</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>[I/R]</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>S</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>S</td>\n",
              "      <td>G</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>N</td>\n",
              "      <td>I</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0017-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "      <td>WGS</td>\n",
              "      <td>True</td>\n",
              "      <td>20.265149</td>\n",
              "      <td>-10.337093</td>\n",
              "      <td>16.565426</td>\n",
              "      <td>-9.832345</td>\n",
              "      <td>CVMNK</td>\n",
              "      <td>WT</td>\n",
              "      <td>ANCSIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNIDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-[A/F]AKA[A/S]</td>\n",
              "      <td>NYD</td>\n",
              "      <td>Pf</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>...</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>C</td>\n",
              "      <td>M</td>\n",
              "      <td>N</td>\n",
              "      <td>K</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>A</td>\n",
              "      <td>Q</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>R</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>S</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>[A/F]</td>\n",
              "      <td>A</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>[A/S]</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>Y</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>N</td>\n",
              "      <td>I</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5 rows × 166 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                      Study  Year     Country  ... PfCRT:326 PfCRT:356 PfMDR2:484\n",
              "SampleId                                       ...                               \n",
              "FP0008-C  1147-PF-MR-CONWAY  2014  Mauritania  ...         N     [T/I]          T\n",
              "FP0009-C  1147-PF-MR-CONWAY  2014  Mauritania  ...         N         T          T\n",
              "FP0015-C  1147-PF-MR-CONWAY  2014  Mauritania  ...         N         I          T\n",
              "FP0016-C  1147-PF-MR-CONWAY  2014  Mauritania  ...         N         I          T\n",
              "FP0017-C  1147-PF-MR-CONWAY  2014  Mauritania  ...         N         I          T\n",
              "\n",
              "[5 rows x 166 columns]"
            ]
          },
          "metadata": {},
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "525c165b"
      },
      "source": [
        "The dataset has 16,720 samples (rows) and 166 columns:"
      ],
      "id": "525c165b"
    },
    {
      "cell_type": "code",
      "metadata": {
        "scrolled": true,
        "id": "3355960d",
        "outputId": "609abbcc-79aa-4575-a97e-473187fd5b82",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "print(list(pf6plus_all))"
      ],
      "id": "3355960d",
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "['Study', 'Year', 'Country', 'AdmDiv1', 'Population', 'Process', 'IncludeInAnalysis', 'Latitude_country', 'Longitude_country', 'Latitude_adm1', 'Longitude_adm1', 'PfCRT', 'Kelch', 'PfDHFR', 'PfEXO', 'PGB', 'Plasmepsin2/3', 'PfDHPS', 'PfMDR1', 'Species', 'Pf3D7_02_v3:376222', 'Pf3D7_02_v3:470013', 'Pf3D7_03_v3:656861', 'Pf3D7_04_v3:110442', 'Pf3D7_04_v3:881571', 'Pf3D7_05_v3:350933', 'Pf3D7_05_v3:369740', 'Pf3D7_06_v3:900278', 'Pf3D7_07_v3:1044052', 'Pf3D7_08_v3:1314831', 'Pf3D7_08_v3:413067', 'Pf3D7_09_v3:900277', 'Pf3D7_11_v3:1018899', 'Pf3D7_11_v3:1815412', 'Pf3D7_13_v3:1056452', 'Pf3D7_13_v3:1466422', 'Pf3D7_14_v3:137622', 'Pf3D7_14_v3:2164225', 'Pf3D7_01_v3:145515', 'Pf3D7_03_v3:548178', 'Pf3D7_04_v3:1102392', 'Pf3D7_04_v3:139051', 'Pf3D7_04_v3:286542', 'Pf3D7_04_v3:529500', 'Pf3D7_05_v3:796714', 'Pf3D7_07_v3:1256331', 'Pf3D7_07_v3:461139', 'Pf3D7_07_v3:619957', 'Pf3D7_08_v3:417335', 'Pf3D7_09_v3:163977', 'Pf3D7_10_v3:317581', 'Pf3D7_10_v3:336274', 'Pf3D7_11_v3:1020397', 'Pf3D7_11_v3:1294107', 'Pf3D7_11_v3:1935227', 'Pf3D7_11_v3:477922', 'Pf3D7_12_v3:1663492', 'Pf3D7_12_v3:2171901', 'Pf3D7_13_v3:1233218', 'Pf3D7_13_v3:1867630', 'Pf3D7_13_v3:2377887', 'Pf3D7_14_v3:2355751', 'Pf3D7_14_v3:3046108', 'Pf3D7_02_v3:529709', 'Pf3D7_02_v3:714480', 'Pf3D7_03_v3:155697', 'Pf3D7_04_v3:1037656', 'Pf3D7_04_v3:648101', 'Pf3D7_05_v3:1204155', 'Pf3D7_06_v3:1282691', 'Pf3D7_06_v3:1289212', 'Pf3D7_07_v3:1066698', 'Pf3D7_07_v3:1213486', 'Pf3D7_07_v3:704373', 'Pf3D7_08_v3:1313202', 'Pf3D7_08_v3:339406', 'Pf3D7_08_v3:701557', 'Pf3D7_09_v3:452690', 'Pf3D7_09_v3:599655', 'Pf3D7_10_v3:1383789', 'Pf3D7_10_v3:1385894', 'Pf3D7_11_v3:1006911', 'Pf3D7_11_v3:1295068', 'Pf3D7_11_v3:1802201', 'Pf3D7_12_v3:1667593', 'Pf3D7_12_v3:1934745', 'Pf3D7_12_v3:858501', 'Pf3D7_13_v3:1419519', 'Pf3D7_13_v3:159086', 'Pf3D7_13_v3:2161975', 'Pf3D7_13_v3:2573828', 'Pf3D7_13_v3:388365', 'Pf3D7_14_v3:2625887', 'Pf3D7_14_v3:3126219', 'Pf3D7_14_v3:438592', 'Pf3D7_01_v3:179347', 'Pf3D7_01_v3:180554', 'Pf3D7_01_v3:283144', 'Pf3D7_01_v3:535211', 'Pf3D7_02_v3:839620', 'Pf3D7_04_v3:426436', 'Pf3D7_04_v3:531138', 'Pf3D7_04_v3:891732', 'Pf3D7_05_v3:172801', 'Pf3D7_06_v3:574938', 'Pf3D7_07_v3:1308383', 'Pf3D7_07_v3:1358910', 'Pf3D7_07_v3:1359218', 'Pf3D7_07_v3:635985', 'Pf3D7_08_v3:1056829', 'Pf3D7_08_v3:150033', 'Pf3D7_08_v3:399774', 'Pf3D7_09_v3:1379145', 'Pf3D7_10_v3:1386850', 'Pf3D7_11_v3:1935031', 'Pf3D7_11_v3:408668', 'Pf3D7_11_v3:828596', 'Pf3D7_12_v3:857245', 'Pf3D7_14_v3:107014', 'Pf3D7_14_v3:1757603', 'Pf3D7_14_v3:2733656', 'GenBarcode', 'Artemisinin', 'Piperaquine', 'DHA-PPQ', 'Chloroquine', 'Pyrimethamine', 'Sulfadoxine', 'S-P', 'S-P-IPTp', 'PfCRT:72', 'PfCRT:74', 'PfCRT:75', 'PfCRT:76', 'PfCRT:93', 'PfCRT:97', 'PfCRT:218', 'PfCRT:220', 'PfCRT:271', 'PfCRT:333', 'PfCRT:353', 'PfCRT:371', 'PfDHFR:16', 'PfDHFR:51', 'PfDHFR:59', 'PfDHFR:108', 'PfDHFR:164', 'PfDHFR:306', 'PfDHPS:436', 'PfDHPS:437', 'PfDHPS:540', 'PfDHPS:581', 'PfDHPS:613', 'PfEXO:415', 'PfMDR1:86', 'PfMDR1:184', 'PfMDR1:1034', 'PfMDR1:1042', 'PfMDR1:1226', 'PfMDR1:1246', 'PfARPS10:127', 'PfARPS10:128', 'PfFD:193', 'PfCRT:326', 'PfCRT:356', 'PfMDR2:484']\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "d2b99797"
      },
      "source": [
        "Even though there is a lot of data to sift through here, in reality the columns can be divided into four main groups:\n",
        "\n",
        "1. Sample metadata\n",
        "1. Barcode SNPs\n",
        "1. Drug resistance SNPs and haplotypes\n",
        "1. Resistance classification\n",
        "\n",
        "Let's explore these groups one at a time."
      ],
      "id": "d2b99797"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "a8cb6fd6"
      },
      "source": [
        "### 1. Sample metadata\n",
        "\n",
        "The metadata included here provide information on each sample, including the study (MalariaGEN partner) it belongs to, year of collection, country, level 1 administrative division, population, the process or type of technology used for sequencing the samples, geographical coordinates, and species. "
      ],
      "id": "a8cb6fd6"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "797d229b",
        "outputId": "1ce285ec-7bdf-428e-b238-76f904986df0",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 235
        }
      },
      "source": [
        "metadata_ls = ['Study','Year','Country','AdmDiv1','Population',\n",
        "               'Process','IncludeInAnalysis',\n",
        "               'Latitude_country','Longitude_country','Latitude_adm1','Longitude_adm1',\n",
        "               'Species']\n",
        "pf6plus_all[metadata_ls[:5]].head()"
      ],
      "id": "797d229b",
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>Study</th>\n",
              "      <th>Year</th>\n",
              "      <th>Country</th>\n",
              "      <th>AdmDiv1</th>\n",
              "      <th>Population</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SampleId</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>FP0008-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0009-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0015-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0016-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0017-C</th>\n",
              "      <td>1147-PF-MR-CONWAY</td>\n",
              "      <td>2014</td>\n",
              "      <td>Mauritania</td>\n",
              "      <td>Hodh el Gharbi</td>\n",
              "      <td>WAF</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "                      Study  Year     Country         AdmDiv1 Population\n",
              "SampleId                                                                \n",
              "FP0008-C  1147-PF-MR-CONWAY  2014  Mauritania  Hodh el Gharbi        WAF\n",
              "FP0009-C  1147-PF-MR-CONWAY  2014  Mauritania  Hodh el Gharbi        WAF\n",
              "FP0015-C  1147-PF-MR-CONWAY  2014  Mauritania  Hodh el Gharbi        WAF\n",
              "FP0016-C  1147-PF-MR-CONWAY  2014  Mauritania  Hodh el Gharbi        WAF\n",
              "FP0017-C  1147-PF-MR-CONWAY  2014  Mauritania  Hodh el Gharbi        WAF"
            ]
          },
          "metadata": {},
          "execution_count": 7
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "684015d2"
      },
      "source": [
        "As you can see here, every sample belongs to a study, which are all described in detail on the MalariaGEN website: explore [Pf6 partner studies](http://ngs.sanger.ac.uk/production/malaria/pfcommunityproject/Pf6/Pf_6_partner_studies.pdf) and [GenRe partner studies](http://ngs.sanger.ac.uk/production/malaria/Resource/29/20200705-GenRe-07-PartnerStudyInformation-0.39.pdf). These descriptions are particularly useful to get context on the study characteristics and epidemiological design, as well as to know all people involved."
      ],
      "id": "684015d2"
    },
    {
      "cell_type": "code",
      "metadata": {
        "scrolled": true,
        "id": "ab6aefce",
        "outputId": "513bb274-56b6-48b3-d90c-a82d358b5b27",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        }
      },
      "source": [
        "pd.options.display.max_colwidth = 100\n",
        "pd.options.display.max_rows = 65\n",
        "pf6plus_all.groupby('Study')['Country'].unique().agg(lambda x: ', '.join(x)).to_frame('Countries')"
      ],
      "id": "ab6aefce",
      "execution_count": 8,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
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              "\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>Countries</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Study</th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>1001-PF-ML-DJIMDE</th>\n",
              "      <td>Mali</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1004-PF-BF-OUEDRAOGO</th>\n",
              "      <td>Burkina Faso</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1006-PF-GM-CONWAY</th>\n",
              "      <td>Gambia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1007-PF-TZ-DUFFY</th>\n",
              "      <td>Tanzania</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1008-PF-SEA-RINGWALD</th>\n",
              "      <td>Vietnam, Myanmar, Laos</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1010-PF-TH-ANDERSON</th>\n",
              "      <td>Thailand</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1011-PF-KH-SU</th>\n",
              "      <td>Cambodia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1012-PF-KH-WHITE</th>\n",
              "      <td>Cambodia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1013-PF-PEGB-BRANCH</th>\n",
              "      <td>Peru</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1014-PF-SSA-SUTHERLAND</th>\n",
              "      <td>Ghana, Mozambique, Uganda, Kenya</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1015-PF-KE-NZILA</th>\n",
              "      <td>Kenya</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1016-PF-TH-NOSTEN</th>\n",
              "      <td>Thailand</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1017-PF-GH-AMENGA-ETEGO</th>\n",
              "      <td>Ghana</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1020-PF-VN-BONI</th>\n",
              "      <td>Vietnam</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1021-PF-PG-MUELLER</th>\n",
              "      <td>Papua New Guinea</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1022-PF-MW-OCHOLLA</th>\n",
              "      <td>Malawi</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1023-PF-CO-ECHEVERRI-GARCIA</th>\n",
              "      <td>Colombia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1024-PF-UG-BOUSEMA</th>\n",
              "      <td>Uganda</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1026-PF-GN-CONWAY</th>\n",
              "      <td>Guinea</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1027-PF-KE-BULL</th>\n",
              "      <td>Kenya</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1031-PF-SEA-PLOWE</th>\n",
              "      <td>Thailand, Cambodia, Bangladesh</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1044-PF-KH-FAIRHURST</th>\n",
              "      <td>Cambodia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1052-PF-TRAC-WHITE</th>\n",
              "      <td>Thailand, Cambodia, Bangladesh, Vietnam, Myanmar, Laos, Democratic Republic of the Congo, Nigeria</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1062-PF-PG-BARRY</th>\n",
              "      <td>Papua New Guinea</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1083-PF-GH-CONWAY</th>\n",
              "      <td>Ghana</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1093-PF-CM-APINJOH</th>\n",
              "      <td>Cameroon</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1094-PF-GH-AMENGA-ETEGO</th>\n",
              "      <td>Ghana</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1095-PF-TZ-ISHENGOMA</th>\n",
              "      <td>Tanzania</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1096-PF-GH-GHANSAH</th>\n",
              "      <td>Ghana</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1097-PF-ML-MAIGA</th>\n",
              "      <td>Mali</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1098-PF-ET-GOLASSA</th>\n",
              "      <td>Ethiopia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1100-PF-CI-YAVO</th>\n",
              "      <td>Côte d'Ivoire</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1101-PF-CD-ONYAMBOKO</th>\n",
              "      <td>Democratic Republic of the Congo</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1102-PF-MG-RANDRIANARIVELOJOSIA</th>\n",
              "      <td>Madagascar</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1103-PF-PDN-GMSN-NGWA</th>\n",
              "      <td>Nigeria</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1107-PF-KEN-KAMAU</th>\n",
              "      <td>Kenya</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1125-PF-TH-NOSTEN</th>\n",
              "      <td>Thailand</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1127-PF-ML-SOULEYMANE</th>\n",
              "      <td>Mali</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1131-PF-BJ-BERTIN</th>\n",
              "      <td>Benin</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1134-PF-ML-CONWAY</th>\n",
              "      <td>Mali</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1135-PF-SN-CONWAY</th>\n",
              "      <td>Senegal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1136-PF-GM-NGWA</th>\n",
              "      <td>Gambia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1137-PF-GM-DALESSANDRO</th>\n",
              "      <td>Gambia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1138-PF-CD-FANELLO</th>\n",
              "      <td>Democratic Republic of the Congo</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1141-PF-GM-CLAESSENS</th>\n",
              "      <td>Gambia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1145-PF-PE-GAMBOA</th>\n",
              "      <td>Peru</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1146-PF-MULTI-PRICE</th>\n",
              "      <td>Indonesia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1147-PF-MR-CONWAY</th>\n",
              "      <td>Mauritania</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1148-PF-BD-MAUDE</th>\n",
              "      <td>Bangladesh</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1151-PF-GH-AMENGA-ETEGO</th>\n",
              "      <td>Ghana</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1172-PF-KH-FAIRHURST-SM</th>\n",
              "      <td>Cambodia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1179-PF-KH-TME-VONSEIDLEIN</th>\n",
              "      <td>Cambodia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1180-PF-TRAC2-DONDORP</th>\n",
              "      <td>Thailand, Bangladesh, Vietnam, Cambodia, Myanmar, Democratic Republic of the Congo, Laos, India</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1181-PF-VN-THUYNHIEN</th>\n",
              "      <td>Vietnam</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1195-PF-TRAC2-DONDORP</th>\n",
              "      <td>Thailand, Cambodia, Vietnam, Myanmar</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1198-PF-METF-NOSTEN</th>\n",
              "      <td>Myanmar, Thailand</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1207-PF-KH-CNM-GENRE</th>\n",
              "      <td>Cambodia</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1208-PF-LA-CMPE-GENRE</th>\n",
              "      <td>Laos</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1209-PF-VN-IMPEQN-GENRE</th>\n",
              "      <td>Vietnam</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1210-PF-TH-MAUDE</th>\n",
              "      <td>Thailand</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1238-PF-VN-NIMPE-GENRE</th>\n",
              "      <td>Vietnam</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "                                                                                                                         Countries\n",
              "Study                                                                                                                             \n",
              "1001-PF-ML-DJIMDE                                                                                                             Mali\n",
              "1004-PF-BF-OUEDRAOGO                                                                                                  Burkina Faso\n",
              "1006-PF-GM-CONWAY                                                                                                           Gambia\n",
              "1007-PF-TZ-DUFFY                                                                                                          Tanzania\n",
              "1008-PF-SEA-RINGWALD                                                                                        Vietnam, Myanmar, Laos\n",
              "1010-PF-TH-ANDERSON                                                                                                       Thailand\n",
              "1011-PF-KH-SU                                                                                                             Cambodia\n",
              "1012-PF-KH-WHITE                                                                                                          Cambodia\n",
              "1013-PF-PEGB-BRANCH                                                                                                           Peru\n",
              "1014-PF-SSA-SUTHERLAND                                                                            Ghana, Mozambique, Uganda, Kenya\n",
              "1015-PF-KE-NZILA                                                                                                             Kenya\n",
              "1016-PF-TH-NOSTEN                                                                                                         Thailand\n",
              "1017-PF-GH-AMENGA-ETEGO                                                                                                      Ghana\n",
              "1020-PF-VN-BONI                                                                                                            Vietnam\n",
              "1021-PF-PG-MUELLER                                                                                                Papua New Guinea\n",
              "1022-PF-MW-OCHOLLA                                                                                                          Malawi\n",
              "1023-PF-CO-ECHEVERRI-GARCIA                                                                                               Colombia\n",
              "1024-PF-UG-BOUSEMA                                                                                                          Uganda\n",
              "1026-PF-GN-CONWAY                                                                                                           Guinea\n",
              "1027-PF-KE-BULL                                                                                                              Kenya\n",
              "1031-PF-SEA-PLOWE                                                                                   Thailand, Cambodia, Bangladesh\n",
              "1044-PF-KH-FAIRHURST                                                                                                      Cambodia\n",
              "1052-PF-TRAC-WHITE               Thailand, Cambodia, Bangladesh, Vietnam, Myanmar, Laos, Democratic Republic of the Congo, Nigeria\n",
              "1062-PF-PG-BARRY                                                                                                  Papua New Guinea\n",
              "1083-PF-GH-CONWAY                                                                                                            Ghana\n",
              "1093-PF-CM-APINJOH                                                                                                        Cameroon\n",
              "1094-PF-GH-AMENGA-ETEGO                                                                                                      Ghana\n",
              "1095-PF-TZ-ISHENGOMA                                                                                                      Tanzania\n",
              "1096-PF-GH-GHANSAH                                                                                                           Ghana\n",
              "1097-PF-ML-MAIGA                                                                                                              Mali\n",
              "1098-PF-ET-GOLASSA                                                                                                        Ethiopia\n",
              "1100-PF-CI-YAVO                                                                                                      Côte d'Ivoire\n",
              "1101-PF-CD-ONYAMBOKO                                                                              Democratic Republic of the Congo\n",
              "1102-PF-MG-RANDRIANARIVELOJOSIA                                                                                         Madagascar\n",
              "1103-PF-PDN-GMSN-NGWA                                                                                                      Nigeria\n",
              "1107-PF-KEN-KAMAU                                                                                                            Kenya\n",
              "1125-PF-TH-NOSTEN                                                                                                         Thailand\n",
              "1127-PF-ML-SOULEYMANE                                                                                                         Mali\n",
              "1131-PF-BJ-BERTIN                                                                                                            Benin\n",
              "1134-PF-ML-CONWAY                                                                                                             Mali\n",
              "1135-PF-SN-CONWAY                                                                                                          Senegal\n",
              "1136-PF-GM-NGWA                                                                                                             Gambia\n",
              "1137-PF-GM-DALESSANDRO                                                                                                      Gambia\n",
              "1138-PF-CD-FANELLO                                                                                Democratic Republic of the Congo\n",
              "1141-PF-GM-CLAESSENS                                                                                                        Gambia\n",
              "1145-PF-PE-GAMBOA                                                                                                             Peru\n",
              "1146-PF-MULTI-PRICE                                                                                                      Indonesia\n",
              "1147-PF-MR-CONWAY                                                                                                       Mauritania\n",
              "1148-PF-BD-MAUDE                                                                                                        Bangladesh\n",
              "1151-PF-GH-AMENGA-ETEGO                                                                                                      Ghana\n",
              "1172-PF-KH-FAIRHURST-SM                                                                                                   Cambodia\n",
              "1179-PF-KH-TME-VONSEIDLEIN                                                                                                Cambodia\n",
              "1180-PF-TRAC2-DONDORP              Thailand, Bangladesh, Vietnam, Cambodia, Myanmar, Democratic Republic of the Congo, Laos, India\n",
              "1181-PF-VN-THUYNHIEN                                                                                                       Vietnam\n",
              "1195-PF-TRAC2-DONDORP                                                                         Thailand, Cambodia, Vietnam, Myanmar\n",
              "1198-PF-METF-NOSTEN                                                                                              Myanmar, Thailand\n",
              "1207-PF-KH-CNM-GENRE                                                                                                      Cambodia\n",
              "1208-PF-LA-CMPE-GENRE                                                                                                         Laos\n",
              "1209-PF-VN-IMPEQN-GENRE                                                                                                    Vietnam\n",
              "1210-PF-TH-MAUDE                                                                                                          Thailand\n",
              "1238-PF-VN-NIMPE-GENRE                                                                                                     Vietnam"
            ]
          },
          "metadata": {},
          "execution_count": 8
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "9792f0b8"
      },
      "source": [
        "If instead of a table, we wanted to have a look at all of the partner studies conducted within this dataset and how many samples they each contributed, can can plot them here, with each color representing a different study:"
      ],
      "id": "9792f0b8"
    },
    {
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        "scrolled": true,
        "id": "373f92e1",
        "outputId": "c7046d7f-c7a2-463b-e458-02cace877c26",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 617
        }
      },
      "source": [
        "plot_samples_per_country_and_study_histogram(pf6plus_all)"
      ],
      "id": "373f92e1",
      "execution_count": 9,
      "outputs": [
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Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    var el = document.getElementById(null);\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\": \"dM3QQsP+wXdHg42wTqW85BjZQdLNNIXqlPw/BgKoExPmTG7ZLML4EGqLMfqHT6ON\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\": \"8x57I4YuIfu8XyZfFo0XVr2WAT8EK4rh/uDe3wF7YuW2FNUSNEpJbsPaB1nJ2fz2\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\": \"3QTqdz9LyAm2i0sG5XTePsHec3UHWwVsrOL68SYRoAXsafvfAyqtQ+h440+qIBhS\"};\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      if (url in hashes) {\n        element.crossOrigin = \"anonymous\";\n        element.integrity = \"sha384-\" + hashes[url];\n      }\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  \n  var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\"];\n  var css_urls = [];\n  \n\n  var inline_js = [\n    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\n    function(Bokeh) {\n    \n    \n    }\n  ];\n\n  function run_inline_js() {\n    \n    if (root.Bokeh !== undefined || force === true) {\n      \n    for (var i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      var cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
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    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7f0b1325"
      },
      "source": [
        "You can filter out samples that fail QC using the `IncludeInAnalysis` filter, which is set to `True` for all the high-quality samples. Using this subset of samples allows you to have higher confidence in your analysis results as these samples have a good amount of reads, are primarily *Plasmodium falciparum* infections (e.g. reduced risk of cross-species reads mapping), are unique in the dataset (e.g. when technical replicates or time series exist). "
      ],
      "id": "7f0b1325"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "9a1d4383",
        "outputId": "0a1ec473-0f79-4b15-c1e3-cba836e8966c",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "pf6plus = pf6plus_all[pf6plus_all['IncludeInAnalysis']]\n",
        "pf6plus_all['IncludeInAnalysis'].value_counts()"
      ],
      "id": "9a1d4383",
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "True     13596\n",
              "False     3124\n",
              "Name: IncludeInAnalysis, dtype: int64"
            ]
          },
          "metadata": {},
          "execution_count": 10
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "f5bd4fb3"
      },
      "source": [
        "We can see that of the 13,596 samples are high quality using the `IncludeInAnalysis` filter, so from here onward, all samples used for subsequent analysis are only high quality samples.  "
      ],
      "id": "f5bd4fb3"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "354a8814"
      },
      "source": [
        "Samples are also conveniently grouped into an analysis `Population` that each consist of parasites with a high degree of genetic similarity, which clusters parasites into 8 geographic regions: Central Africa (CAF), East Africa (EAF), Eastern S.E. Asia (ESEA), Oceania (OCE), South America (SAM), South Asia (SAS), West Africa (WAF), Western S.E. Asia (WSEA). The countries that belong to each analysis `Population` are seen below. "
      ],
      "id": "354a8814"
    },
    {
      "cell_type": "code",
      "metadata": {
        "scrolled": false,
        "id": "c53a9f39",
        "outputId": "4f96e1ac-a229-423d-bbdc-9a150a5c2339",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        }
      },
      "source": [
        "pf6plus.groupby(['Population', 'Country']).size().to_frame('Number of samples')"
      ],
      "id": "c53a9f39",
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
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              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th>Number of samples</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Population</th>\n",
              "      <th>Country</th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>CAF</th>\n",
              "      <th>Democratic Republic of the Congo</th>\n",
              "      <td>464</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th rowspan=\"7\" valign=\"top\">EAF</th>\n",
              "      <th>Ethiopia</th>\n",
              "      <td>21</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Kenya</th>\n",
              "      <td>110</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Madagascar</th>\n",
              "      <td>24</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Malawi</th>\n",
              "      <td>254</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Mozambique</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Tanzania</th>\n",
              "      <td>316</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Uganda</th>\n",
              "      <td>13</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th rowspan=\"4\" valign=\"top\">ESEA</th>\n",
              "      <th>Cambodia</th>\n",
              "      <td>1875</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Laos</th>\n",
              "      <td>1518</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Thailand</th>\n",
              "      <td>123</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Vietnam</th>\n",
              "      <td>2302</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th rowspan=\"2\" valign=\"top\">OCE</th>\n",
              "      <th>Indonesia</th>\n",
              "      <td>80</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Papua New Guinea</th>\n",
              "      <td>121</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th rowspan=\"2\" valign=\"top\">SAM</th>\n",
              "      <th>Colombia</th>\n",
              "      <td>16</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Peru</th>\n",
              "      <td>21</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th rowspan=\"2\" valign=\"top\">SAS</th>\n",
              "      <th>Bangladesh</th>\n",
              "      <td>1770</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>India</th>\n",
              "      <td>280</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th rowspan=\"11\" valign=\"top\">WAF</th>\n",
              "      <th>Benin</th>\n",
              "      <td>36</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Burkina Faso</th>\n",
              "      <td>56</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Cameroon</th>\n",
              "      <td>235</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Côte d'Ivoire</th>\n",
              "      <td>70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Gambia</th>\n",
              "      <td>219</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Ghana</th>\n",
              "      <td>851</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Guinea</th>\n",
              "      <td>149</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Mali</th>\n",
              "      <td>426</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Mauritania</th>\n",
              "      <td>76</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Nigeria</th>\n",
              "      <td>29</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Senegal</th>\n",
              "      <td>84</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th rowspan=\"2\" valign=\"top\">WSEA</th>\n",
              "      <th>Myanmar</th>\n",
              "      <td>1160</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Thailand</th>\n",
              "      <td>896</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "                                             Number of samples\n",
              "Population Country                                            \n",
              "CAF        Democratic Republic of the Congo                464\n",
              "EAF        Ethiopia                                         21\n",
              "           Kenya                                           110\n",
              "           Madagascar                                       24\n",
              "           Malawi                                          254\n",
              "           Mozambique                                        1\n",
              "           Tanzania                                        316\n",
              "           Uganda                                           13\n",
              "ESEA       Cambodia                                       1875\n",
              "           Laos                                           1518\n",
              "           Thailand                                        123\n",
              "           Vietnam                                        2302\n",
              "OCE        Indonesia                                        80\n",
              "           Papua New Guinea                                121\n",
              "SAM        Colombia                                         16\n",
              "           Peru                                             21\n",
              "SAS        Bangladesh                                     1770\n",
              "           India                                           280\n",
              "WAF        Benin                                            36\n",
              "           Burkina Faso                                     56\n",
              "           Cameroon                                        235\n",
              "           Côte d'Ivoire                                    70\n",
              "           Gambia                                          219\n",
              "           Ghana                                           851\n",
              "           Guinea                                          149\n",
              "           Mali                                            426\n",
              "           Mauritania                                       76\n",
              "           Nigeria                                          29\n",
              "           Senegal                                          84\n",
              "WSEA       Myanmar                                        1160\n",
              "           Thailand                                        896"
            ]
          },
          "metadata": {},
          "execution_count": 11
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "31e6679a"
      },
      "source": [
        "You can also see what `Process` (or technology) each sample was generated with, as this dataset consists of genotyping data from the following: \n",
        "\n",
        "- whole-genome sequencing\n",
        "- amplicon sequencing\n",
        "- Agena genotyping\n"
      ],
      "id": "31e6679a"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "522bbeb5",
        "outputId": "1befe163-615e-429c-c213-29dfb38bb77b",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 204
        }
      },
      "source": [
        "pf6plus_all.groupby('Process').size().to_frame('Number of samples')"
      ],
      "id": "522bbeb5",
      "execution_count": 12,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>Number of samples</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Process</th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>Agena</th>\n",
              "      <td>6150</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>AmpSeq-V1</th>\n",
              "      <td>1041</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>AmpSeq-V2</th>\n",
              "      <td>2432</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>WGS</th>\n",
              "      <td>7097</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "           Number of samples\n",
              "Process                     \n",
              "Agena                   6150\n",
              "AmpSeq-V1               1041\n",
              "AmpSeq-V2               2432\n",
              "WGS                     7097"
            ]
          },
          "metadata": {},
          "execution_count": 12
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "01afe84a"
      },
      "source": [
        "### 2. Barcode SNPs\n",
        "\n",
        "Includes genotypes on 101 SNPs with medium/high global frequency."
      ],
      "id": "01afe84a"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "7b637bfd",
        "outputId": "ab611bad-b332-4cca-f04d-0a7b2d871a76",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 301
        }
      },
      "source": [
        "barcode_ls = [col for col in list(pf6plus.columns.values.tolist()) if col.startswith('Pf3D7_')]\n",
        "print(len(barcode_ls))\n",
        "pf6plus[barcode_ls].head()"
      ],
      "id": "7b637bfd",
      "execution_count": 13,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "101\n"
          ]
        },
        {
          "output_type": "execute_result",
          "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>Pf3D7_02_v3:376222</th>\n",
              "      <th>Pf3D7_02_v3:470013</th>\n",
              "      <th>Pf3D7_03_v3:656861</th>\n",
              "      <th>Pf3D7_04_v3:110442</th>\n",
              "      <th>Pf3D7_04_v3:881571</th>\n",
              "      <th>Pf3D7_05_v3:350933</th>\n",
              "      <th>Pf3D7_05_v3:369740</th>\n",
              "      <th>Pf3D7_06_v3:900278</th>\n",
              "      <th>Pf3D7_07_v3:1044052</th>\n",
              "      <th>Pf3D7_08_v3:1314831</th>\n",
              "      <th>Pf3D7_08_v3:413067</th>\n",
              "      <th>Pf3D7_09_v3:900277</th>\n",
              "      <th>Pf3D7_11_v3:1018899</th>\n",
              "      <th>Pf3D7_11_v3:1815412</th>\n",
              "      <th>Pf3D7_13_v3:1056452</th>\n",
              "      <th>Pf3D7_13_v3:1466422</th>\n",
              "      <th>Pf3D7_14_v3:137622</th>\n",
              "      <th>Pf3D7_14_v3:2164225</th>\n",
              "      <th>Pf3D7_01_v3:145515</th>\n",
              "      <th>Pf3D7_03_v3:548178</th>\n",
              "      <th>Pf3D7_04_v3:1102392</th>\n",
              "      <th>Pf3D7_04_v3:139051</th>\n",
              "      <th>Pf3D7_04_v3:286542</th>\n",
              "      <th>Pf3D7_04_v3:529500</th>\n",
              "      <th>Pf3D7_05_v3:796714</th>\n",
              "      <th>Pf3D7_07_v3:1256331</th>\n",
              "      <th>Pf3D7_07_v3:461139</th>\n",
              "      <th>Pf3D7_07_v3:619957</th>\n",
              "      <th>Pf3D7_08_v3:417335</th>\n",
              "      <th>Pf3D7_09_v3:163977</th>\n",
              "      <th>Pf3D7_10_v3:317581</th>\n",
              "      <th>Pf3D7_10_v3:336274</th>\n",
              "      <th>Pf3D7_11_v3:1020397</th>\n",
              "      <th>Pf3D7_11_v3:1294107</th>\n",
              "      <th>Pf3D7_11_v3:1935227</th>\n",
              "      <th>Pf3D7_11_v3:477922</th>\n",
              "      <th>Pf3D7_12_v3:1663492</th>\n",
              "      <th>Pf3D7_12_v3:2171901</th>\n",
              "      <th>Pf3D7_13_v3:1233218</th>\n",
              "      <th>Pf3D7_13_v3:1867630</th>\n",
              "      <th>...</th>\n",
              "      <th>Pf3D7_11_v3:1006911</th>\n",
              "      <th>Pf3D7_11_v3:1295068</th>\n",
              "      <th>Pf3D7_11_v3:1802201</th>\n",
              "      <th>Pf3D7_12_v3:1667593</th>\n",
              "      <th>Pf3D7_12_v3:1934745</th>\n",
              "      <th>Pf3D7_12_v3:858501</th>\n",
              "      <th>Pf3D7_13_v3:1419519</th>\n",
              "      <th>Pf3D7_13_v3:159086</th>\n",
              "      <th>Pf3D7_13_v3:2161975</th>\n",
              "      <th>Pf3D7_13_v3:2573828</th>\n",
              "      <th>Pf3D7_13_v3:388365</th>\n",
              "      <th>Pf3D7_14_v3:2625887</th>\n",
              "      <th>Pf3D7_14_v3:3126219</th>\n",
              "      <th>Pf3D7_14_v3:438592</th>\n",
              "      <th>Pf3D7_01_v3:179347</th>\n",
              "      <th>Pf3D7_01_v3:180554</th>\n",
              "      <th>Pf3D7_01_v3:283144</th>\n",
              "      <th>Pf3D7_01_v3:535211</th>\n",
              "      <th>Pf3D7_02_v3:839620</th>\n",
              "      <th>Pf3D7_04_v3:426436</th>\n",
              "      <th>Pf3D7_04_v3:531138</th>\n",
              "      <th>Pf3D7_04_v3:891732</th>\n",
              "      <th>Pf3D7_05_v3:172801</th>\n",
              "      <th>Pf3D7_06_v3:574938</th>\n",
              "      <th>Pf3D7_07_v3:1308383</th>\n",
              "      <th>Pf3D7_07_v3:1358910</th>\n",
              "      <th>Pf3D7_07_v3:1359218</th>\n",
              "      <th>Pf3D7_07_v3:635985</th>\n",
              "      <th>Pf3D7_08_v3:1056829</th>\n",
              "      <th>Pf3D7_08_v3:150033</th>\n",
              "      <th>Pf3D7_08_v3:399774</th>\n",
              "      <th>Pf3D7_09_v3:1379145</th>\n",
              "      <th>Pf3D7_10_v3:1386850</th>\n",
              "      <th>Pf3D7_11_v3:1935031</th>\n",
              "      <th>Pf3D7_11_v3:408668</th>\n",
              "      <th>Pf3D7_11_v3:828596</th>\n",
              "      <th>Pf3D7_12_v3:857245</th>\n",
              "      <th>Pf3D7_14_v3:107014</th>\n",
              "      <th>Pf3D7_14_v3:1757603</th>\n",
              "      <th>Pf3D7_14_v3:2733656</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SampleId</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>FP0008-C</th>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>...</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0009-C</th>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>...</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0015-C</th>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>...</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0016-C</th>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>...</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>X</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0017-C</th>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>G</td>\n",
              "      <td>...</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>A</td>\n",
              "      <td>G</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>N</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>C</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>C</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5 rows × 101 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "         Pf3D7_02_v3:376222  ... Pf3D7_14_v3:2733656\n",
              "SampleId                     ...                    \n",
              "FP0008-C                  G  ...                   T\n",
              "FP0009-C                  G  ...                   C\n",
              "FP0015-C                  G  ...                   N\n",
              "FP0016-C                  A  ...                   C\n",
              "FP0017-C                  G  ...                   N\n",
              "\n",
              "[5 rows x 101 columns]"
            ]
          },
          "metadata": {},
          "execution_count": 13
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "758e3884"
      },
      "source": [
        "Let's look at the frequency of one of these SNPs:"
      ],
      "id": "758e3884"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "0453b581",
        "outputId": "4ff26328-be5c-40e3-ea74-0e6e9bef10fd",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "pf6plus[barcode_ls[0]].value_counts()"
      ],
      "id": "0453b581",
      "execution_count": 14,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "A    6960\n",
              "G    4741\n",
              "N    1026\n",
              "X     869\n",
              "Name: Pf3D7_02_v3:376222, dtype: int64"
            ]
          },
          "metadata": {},
          "execution_count": 14
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "011828ac"
      },
      "source": [
        "If you want to explore all the SNPs together for each of the samples, you can use the `GenBarcode` field:"
      ],
      "id": "011828ac"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "f3c57686",
        "outputId": "6f8d4e63-ae6c-4bcc-e14a-381d25b4cf1f",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "pf6plus['GenBarcode'].head()"
      ],
      "id": "f3c57686",
      "execution_count": 15,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "SampleId\n",
              "FP0008-C    GGTTGGTGNNNATGCGTANCATGAGCNCCNTATCNTGATGCANTTANANGAAGNNAGNGNNAGGCGCNATCCNCAGGGNCATAGNCATCATCGNTT...\n",
              "FP0009-C    GATCAGTGTGAGCCTGTGTCATGAATAGCTAATTATGATCATCTTAAAAAAAGATATGGATAAGTACTAAACGTAGAGCTATAACTGTCATCGCTA...\n",
              "FP0015-C    GATCGGTGCNGANGTGTATCAGGGNTGGCTAGNCATGATGATTTTATGNAAAGANANACATAAGCGNCGTACCNAGNGTCATAGACAATNTNATTT...\n",
              "FP0016-C    AGTCGGTGCGNATGTGCANCAGGAATGGCTANCCATGACGATTTTANGCAAAAATAXGGATAAGCGCNGTNCCCAGGXTCAGAGNTAATATCGTTT...\n",
              "FP0017-C    GGTTAATGCAGANNTGTGTCATGANTGNCCAGTCACNTCGCATTTAAGAAANGNTAGGGATAAGTAANAAACNNAGGGTTAGAAANNACANCACTT...\n",
              "Name: GenBarcode, dtype: object"
            ]
          },
          "metadata": {},
          "execution_count": 15
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "90361a44"
      },
      "source": [
        "### 3.  Drug resistance SNPs and haplotypes\n",
        "\n",
        "Information on 36 SNPs from 10 genes associated with or relevant for antimalarial resistance:\n"
      ],
      "id": "90361a44"
    },
    {
      "cell_type": "code",
      "metadata": {
        "scrolled": true,
        "id": "3ee08b0b",
        "outputId": "02e63cea-3b55-453d-ab42-b18ef20e16be",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 255
        }
      },
      "source": [
        "dr_snp_ls = ['PfCRT:72','PfCRT:74','PfCRT:75','PfCRT:76','PfCRT:93','PfCRT:97','PfCRT:218','PfCRT:220',\n",
        "          'PfCRT:271', 'PfCRT:326','PfCRT:333', 'PfCRT:353', 'PfCRT:356', 'PfCRT:371',\n",
        "          'PfDHFR:16','PfDHFR:51','PfDHFR:59','PfDHFR:108','PfDHFR:164','PfDHFR:306',\n",
        "          'PfDHPS:436','PfDHPS:437','PfDHPS:540','PfDHPS:581','PfDHPS:613',\n",
        "          'PfEXO:415',\n",
        "          'PfMDR1:86','PfMDR1:184','PfMDR1:1034','PfMDR1:1042','PfMDR1:1226','PfMDR1:1246',\n",
        "          'PfARPS10:127','PfARPS10:128','PfFD:193','PfMDR2:484']\n",
        "\n",
        "pf6plus[dr_snp_ls].head()"
      ],
      "id": "3ee08b0b",
      "execution_count": 16,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>PfCRT:72</th>\n",
              "      <th>PfCRT:74</th>\n",
              "      <th>PfCRT:75</th>\n",
              "      <th>PfCRT:76</th>\n",
              "      <th>PfCRT:93</th>\n",
              "      <th>PfCRT:97</th>\n",
              "      <th>PfCRT:218</th>\n",
              "      <th>PfCRT:220</th>\n",
              "      <th>PfCRT:271</th>\n",
              "      <th>PfCRT:326</th>\n",
              "      <th>PfCRT:333</th>\n",
              "      <th>PfCRT:353</th>\n",
              "      <th>PfCRT:356</th>\n",
              "      <th>PfCRT:371</th>\n",
              "      <th>PfDHFR:16</th>\n",
              "      <th>PfDHFR:51</th>\n",
              "      <th>PfDHFR:59</th>\n",
              "      <th>PfDHFR:108</th>\n",
              "      <th>PfDHFR:164</th>\n",
              "      <th>PfDHFR:306</th>\n",
              "      <th>PfDHPS:436</th>\n",
              "      <th>PfDHPS:437</th>\n",
              "      <th>PfDHPS:540</th>\n",
              "      <th>PfDHPS:581</th>\n",
              "      <th>PfDHPS:613</th>\n",
              "      <th>PfEXO:415</th>\n",
              "      <th>PfMDR1:86</th>\n",
              "      <th>PfMDR1:184</th>\n",
              "      <th>PfMDR1:1034</th>\n",
              "      <th>PfMDR1:1042</th>\n",
              "      <th>PfMDR1:1226</th>\n",
              "      <th>PfMDR1:1246</th>\n",
              "      <th>PfARPS10:127</th>\n",
              "      <th>PfARPS10:128</th>\n",
              "      <th>PfFD:193</th>\n",
              "      <th>PfMDR2:484</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SampleId</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>FP0008-C</th>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>[T/K]</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>[S/A]</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>[T/I]</td>\n",
              "      <td>[I/R]</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>[S/N]</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>[A/S]</td>\n",
              "      <td>[A/G]</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>[F/Y]</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0009-C</th>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>T</td>\n",
              "      <td>I</td>\n",
              "      <td>A</td>\n",
              "      <td>I</td>\n",
              "      <td>R</td>\n",
              "      <td>N</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>Y</td>\n",
              "      <td>F</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>Y</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0015-C</th>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>T</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>I</td>\n",
              "      <td>I</td>\n",
              "      <td>A</td>\n",
              "      <td>I</td>\n",
              "      <td>R</td>\n",
              "      <td>N</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>[A/S]</td>\n",
              "      <td>[A/G]</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>[F/Y]</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0016-C</th>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>-</td>\n",
              "      <td>[T/K]</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>I</td>\n",
              "      <td>[I/R]</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>S</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>S</td>\n",
              "      <td>G</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>A</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0017-C</th>\n",
              "      <td>C</td>\n",
              "      <td>M</td>\n",
              "      <td>N</td>\n",
              "      <td>K</td>\n",
              "      <td>T</td>\n",
              "      <td>H</td>\n",
              "      <td>I</td>\n",
              "      <td>A</td>\n",
              "      <td>Q</td>\n",
              "      <td>N</td>\n",
              "      <td>T</td>\n",
              "      <td>G</td>\n",
              "      <td>I</td>\n",
              "      <td>R</td>\n",
              "      <td>A</td>\n",
              "      <td>N</td>\n",
              "      <td>C</td>\n",
              "      <td>S</td>\n",
              "      <td>I</td>\n",
              "      <td>S</td>\n",
              "      <td>[A/F]</td>\n",
              "      <td>A</td>\n",
              "      <td>K</td>\n",
              "      <td>A</td>\n",
              "      <td>[A/S]</td>\n",
              "      <td>E</td>\n",
              "      <td>N</td>\n",
              "      <td>Y</td>\n",
              "      <td>S</td>\n",
              "      <td>N</td>\n",
              "      <td>F</td>\n",
              "      <td>D</td>\n",
              "      <td>V</td>\n",
              "      <td>D</td>\n",
              "      <td>D</td>\n",
              "      <td>T</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "         PfCRT:72 PfCRT:74 PfCRT:75  ... PfARPS10:128 PfFD:193 PfMDR2:484\n",
              "SampleId                             ...                                 \n",
              "FP0008-C        -        -        -  ...            D        D          T\n",
              "FP0009-C        -        -        -  ...            D        D          T\n",
              "FP0015-C        -        -        -  ...            D        D          T\n",
              "FP0016-C        -        -        -  ...            D        D          T\n",
              "FP0017-C        C        M        N  ...            D        D          T\n",
              "\n",
              "[5 rows x 36 columns]"
            ]
          },
          "metadata": {},
          "execution_count": 16
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "005dbec8"
      },
      "source": [
        "Information on common haplotypes from 8 genes associated with or relevant for antimalarial resistance:"
      ],
      "id": "005dbec8"
    },
    {
      "cell_type": "code",
      "metadata": {
        "scrolled": true,
        "id": "fa826101",
        "outputId": "75160f85-4241-42a1-b187-4cb2f3089912",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 235
        }
      },
      "source": [
        "dr_hap_ls = ['PfCRT','Kelch','PfDHFR','PfEXO','PGB','Plasmepsin2/3','PfDHPS','PfMDR1']\n",
        "pf6plus[dr_hap_ls].head()"
      ],
      "id": "fa826101",
      "execution_count": 17,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>PfCRT</th>\n",
              "      <th>Kelch</th>\n",
              "      <th>PfDHFR</th>\n",
              "      <th>PfEXO</th>\n",
              "      <th>PGB</th>\n",
              "      <th>Plasmepsin2/3</th>\n",
              "      <th>PfDHPS</th>\n",
              "      <th>PfMDR1</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SampleId</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>FP0008-C</th>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>ANC[S/N]IS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDN[T/I]DT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-[A/S][A/G]KAA</td>\n",
              "      <td>N[F/Y]D</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0009-C</th>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>AIRNIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNTDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-AAKAA</td>\n",
              "      <td>YFY</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0015-C</th>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>AIRNIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNIDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-[A/S][A/G]KAA</td>\n",
              "      <td>N[F/Y]D</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0016-C</th>\n",
              "      <td>-----</td>\n",
              "      <td>WT</td>\n",
              "      <td>ANCSIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNIDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-SGKAA</td>\n",
              "      <td>NFD</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0017-C</th>\n",
              "      <td>CVMNK</td>\n",
              "      <td>WT</td>\n",
              "      <td>ANCSIS</td>\n",
              "      <td>E</td>\n",
              "      <td>VDNIDT</td>\n",
              "      <td>WT</td>\n",
              "      <td>-[A/F]AKA[A/S]</td>\n",
              "      <td>NYD</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "          PfCRT Kelch      PfDHFR  ... Plasmepsin2/3          PfDHPS   PfMDR1\n",
              "SampleId                           ...                                       \n",
              "FP0008-C  -----    WT  ANC[S/N]IS  ...            WT  -[A/S][A/G]KAA  N[F/Y]D\n",
              "FP0009-C  -----    WT      AIRNIS  ...            WT          -AAKAA      YFY\n",
              "FP0015-C  -----    WT      AIRNIS  ...            WT  -[A/S][A/G]KAA  N[F/Y]D\n",
              "FP0016-C  -----    WT      ANCSIS  ...            WT          -SGKAA      NFD\n",
              "FP0017-C  CVMNK    WT      ANCSIS  ...            WT  -[A/F]AKA[A/S]      NYD\n",
              "\n",
              "[5 rows x 8 columns]"
            ]
          },
          "metadata": {},
          "execution_count": 17
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7f3c12e6"
      },
      "source": [
        "### 4. Drug resistance classification (*aka* phenotypes)\n",
        "\n",
        "Each sample is classified into `Resistant`, `Sensitive`, or `Undetermined` to eight major antimalarial drugs or combination therapy based on well-recognised markers of resistance. Details of the methods can be found in the Pf6 and GenRe-Mekong publications."
      ],
      "id": "7f3c12e6"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "61c0b3df",
        "outputId": "1b43979d-5c19-4b61-e6e8-f161007ce9fa",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 235
        }
      },
      "source": [
        "drugs_ls = ['Artemisinin','Piperaquine','DHA-PPQ','Chloroquine','Pyrimethamine','Sulfadoxine','S-P','S-P-IPTp']\n",
        "pf6plus[drugs_ls].head()"
      ],
      "id": "61c0b3df",
      "execution_count": 18,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>Artemisinin</th>\n",
              "      <th>Piperaquine</th>\n",
              "      <th>DHA-PPQ</th>\n",
              "      <th>Chloroquine</th>\n",
              "      <th>Pyrimethamine</th>\n",
              "      <th>Sulfadoxine</th>\n",
              "      <th>S-P</th>\n",
              "      <th>S-P-IPTp</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>SampleId</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>FP0008-C</th>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0009-C</th>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0015-C</th>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0016-C</th>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Undetermined</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Resistant</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>FP0017-C</th>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "      <td>Sensitive</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "         Artemisinin Piperaquine    DHA-PPQ  ...   Sulfadoxine        S-P   S-P-IPTp\n",
              "SampleId                                     ...                                    \n",
              "FP0008-C   Sensitive   Sensitive  Sensitive  ...  Undetermined  Sensitive  Sensitive\n",
              "FP0009-C   Sensitive   Sensitive  Sensitive  ...     Sensitive  Resistant  Sensitive\n",
              "FP0015-C   Sensitive   Sensitive  Sensitive  ...  Undetermined  Resistant  Sensitive\n",
              "FP0016-C   Sensitive   Sensitive  Sensitive  ...     Resistant  Sensitive  Sensitive\n",
              "FP0017-C   Sensitive   Sensitive  Sensitive  ...     Sensitive  Sensitive  Sensitive\n",
              "\n",
              "[5 rows x 8 columns]"
            ]
          },
          "metadata": {},
          "execution_count": 18
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "8fd8aabf"
      },
      "source": [
        "---"
      ],
      "id": "8fd8aabf"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "af1285c3"
      },
      "source": [
        "## Geographical distribution of samples in Pf6+\n",
        "\n",
        "The plots below show the geographical distribution of data, and how combining them can provide a greater global coverage.\n",
        "\n",
        "Click on the pin to find out more about the data collected at each site. "
      ],
      "id": "af1285c3"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "48f0d422"
      },
      "source": [
        "#### Samples in the Pf6 data release"
      ],
      "id": "48f0d422"
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 808
        },
        "id": "507fa41e",
        "outputId": "49399c44-799c-45dd-e9d4-14b7811f35ae"
      },
      "source": [
        "map_samples(pf6plus, 'Pf6')"
      ],
      "id": "507fa41e",
      "execution_count": 19,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><span style=\"color:#565656\">Make this Notebook Trusted to load map: File -> Trust Notebook</span><iframe src=\"about:blank\" style=\"position:absolute;width:100%;height:100%;left:0;top:0;border:none !important;\" 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            ],
            "text/plain": [
              "<folium.folium.Map at 0x7efe0243d410>"
            ]
          },
          "metadata": {},
          "execution_count": 19
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "909030a7"
      },
      "source": [
        "#### Samples in the GenRe-Mekong data release"
      ],
      "id": "909030a7"
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 808
        },
        "id": "b97b02e5",
        "outputId": "ea67bea0-a056-44cc-80ed-054d49314de3"
      },
      "source": [
        "map_samples(pf6plus, 'GenRe')"
      ],
      "id": "b97b02e5",
      "execution_count": 20,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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            ],
            "text/plain": [
              "<folium.folium.Map at 0x7efe01e12b50>"
            ]
          },
          "metadata": {},
          "execution_count": 20
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "07fb4740"
      },
      "source": [
        "#### Samples in Pf6+ (union of the above)"
      ],
      "id": "07fb4740"
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 808
        },
        "id": "1a20716c",
        "scrolled": true,
        "outputId": "28871384-3d9a-46b1-83e7-56c4a8170c33"
      },
      "source": [
        "map_samples(pf6plus, 'Pf6+')"
      ],
      "id": "1a20716c",
      "execution_count": 21,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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onload=\"this.contentDocument.open();this.contentDocument.write(    decodeURIComponent(this.getAttribute('data-html')));this.contentDocument.close();\" allowfullscreen webkitallowfullscreen mozallowfullscreen></iframe></div></div>"
            ],
            "text/plain": [
              "<folium.folium.Map at 0x7efe0088b990>"
            ]
          },
          "metadata": {},
          "execution_count": 21
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "6d74d26a"
      },
      "source": [
        "---"
      ],
      "id": "6d74d26a"
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7dc7be2f"
      },
      "source": [
        "## Temporal distribution of samples on Pf6+\n",
        "\n",
        "As for the geographical coverage above, combining the two resources allows for a wider and more complete temporal spread."
      ],
      "id": "7dc7be2f"
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 617
        },
        "id": "f9e7280f",
        "scrolled": false,
        "outputId": "0e7b4790-4822-44da-9074-09679f70e15e"
      },
      "source": [
        "plot_temporal_samples_histogram(pf6plus)"
      ],
      "id": "f9e7280f",
      "execution_count": 22,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "application/javascript": [
              "\n",
              "(function(root) {\n",
              "  function now() {\n",
              "    return new Date();\n",
              "  }\n",
              "\n",
              "  var force = true;\n",
              "\n",
              "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
              "    root._bokeh_onload_callbacks = [];\n",
              "    root._bokeh_is_loading = undefined;\n",
              "  }\n",
              "\n",
              "  var JS_MIME_TYPE = 'application/javascript';\n",
              "  var HTML_MIME_TYPE = 'text/html';\n",
              "  var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
              "  var CLASS_NAME = 'output_bokeh rendered_html';\n",
              "\n",
              "  /**\n",
              "   * Render data to the DOM node\n",
              "   */\n",
              "  function render(props, node) {\n",
              "    var script = document.createElement(\"script\");\n",
              "    node.appendChild(script);\n",
              "  }\n",
              "\n",
              "  /**\n",
              "   * Handle when an output is cleared or removed\n",
              "   */\n",
              "  function handleClearOutput(event, handle) {\n",
              "    var cell = handle.cell;\n",
              "\n",
              "    var id = cell.output_area._bokeh_element_id;\n",
              "    var server_id = cell.output_area._bokeh_server_id;\n",
              "    // Clean up Bokeh references\n",
              "    if (id != null && id in Bokeh.index) {\n",
              "      Bokeh.index[id].model.document.clear();\n",
              "      delete Bokeh.index[id];\n",
              "    }\n",
              "\n",
              "    if (server_id !== undefined) {\n",
              "      // Clean up Bokeh references\n",
              "      var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
              "      cell.notebook.kernel.execute(cmd, {\n",
              "        iopub: {\n",
              "          output: function(msg) {\n",
              "            var id = msg.content.text.trim();\n",
              "            if (id in Bokeh.index) {\n",
              "              Bokeh.index[id].model.document.clear();\n",
              "              delete Bokeh.index[id];\n",
              "            }\n",
              "          }\n",
              "        }\n",
              "      });\n",
              "      // Destroy server and session\n",
              "      var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
              "      cell.notebook.kernel.execute(cmd);\n",
              "    }\n",
              "  }\n",
              "\n",
              "  /**\n",
              "   * Handle when a new output is added\n",
              "   */\n",
              "  function handleAddOutput(event, handle) {\n",
              "    var output_area = handle.output_area;\n",
              "    var output = handle.output;\n",
              "\n",
              "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
              "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
              "      return\n",
              "    }\n",
              "\n",
              "    var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
              "\n",
              "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
              "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
              "      // store reference to embed id on output_area\n",
              "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
              "    }\n",
              "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
              "      var bk_div = document.createElement(\"div\");\n",
              "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
              "      var script_attrs = bk_div.children[0].attributes;\n",
              "      for (var i = 0; i < script_attrs.length; i++) {\n",
              "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
              "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
              "      }\n",
              "      // store reference to server id on output_area\n",
              "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
              "    }\n",
              "  }\n",
              "\n",
              "  function register_renderer(events, OutputArea) {\n",
              "\n",
              "    function append_mime(data, metadata, element) {\n",
              "      // create a DOM node to render to\n",
              "      var toinsert = this.create_output_subarea(\n",
              "        metadata,\n",
              "        CLASS_NAME,\n",
              "        EXEC_MIME_TYPE\n",
              "      );\n",
              "      this.keyboard_manager.register_events(toinsert);\n",
              "      // Render to node\n",
              "      var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
              "      render(props, toinsert[toinsert.length - 1]);\n",
              "      element.append(toinsert);\n",
              "      return toinsert\n",
              "    }\n",
              "\n",
              "    /* Handle when an output is cleared or removed */\n",
              "    events.on('clear_output.CodeCell', handleClearOutput);\n",
              "    events.on('delete.Cell', handleClearOutput);\n",
              "\n",
              "    /* Handle when a new output is added */\n",
              "    events.on('output_added.OutputArea', handleAddOutput);\n",
              "\n",
              "    /**\n",
              "     * Register the mime type and append_mime function with output_area\n",
              "     */\n",
              "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
              "      /* Is output safe? */\n",
              "      safe: true,\n",
              "      /* Index of renderer in `output_area.display_order` */\n",
              "      index: 0\n",
              "    });\n",
              "  }\n",
              "\n",
              "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
              "  if (root.Jupyter !== undefined) {\n",
              "    var events = require('base/js/events');\n",
              "    var OutputArea = require('notebook/js/outputarea').OutputArea;\n",
              "\n",
              "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
              "      register_renderer(events, OutputArea);\n",
              "    }\n",
              "  }\n",
              "\n",
              "  \n",
              "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
              "    root._bokeh_timeout = Date.now() + 5000;\n",
              "    root._bokeh_failed_load = false;\n",
              "  }\n",
              "\n",
              "  var NB_LOAD_WARNING = {'data': {'text/html':\n",
              "     \"<div style='background-color: #fdd'>\\n\"+\n",
              "     \"<p>\\n\"+\n",
              "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
              "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
              "     \"</p>\\n\"+\n",
              "     \"<ul>\\n\"+\n",
              "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
              "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
              "     \"</ul>\\n\"+\n",
              "     \"<code>\\n\"+\n",
              "     \"from bokeh.resources import INLINE\\n\"+\n",
              "     \"output_notebook(resources=INLINE)\\n\"+\n",
              "     \"</code>\\n\"+\n",
              "     \"</div>\"}};\n",
              "\n",
              "  function display_loaded() {\n",
              "    var el = document.getElementById(null);\n",
              "    if (el != null) {\n",
              "      el.textContent = \"BokehJS is loading...\";\n",
              "    }\n",
              "    if (root.Bokeh !== undefined) {\n",
              "      if (el != null) {\n",
              "        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
              "      }\n",
              "    } else if (Date.now() < root._bokeh_timeout) {\n",
              "      setTimeout(display_loaded, 100)\n",
              "    }\n",
              "  }\n",
              "\n",
              "\n",
              "  function run_callbacks() {\n",
              "    try {\n",
              "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
              "        if (callback != null)\n",
              "          callback();\n",
              "      });\n",
              "    } finally {\n",
              "      delete root._bokeh_onload_callbacks\n",
              "    }\n",
              "    console.debug(\"Bokeh: all callbacks have finished\");\n",
              "  }\n",
              "\n",
              "  function load_libs(css_urls, js_urls, callback) {\n",
              "    if (css_urls == null) css_urls = [];\n",
              "    if (js_urls == null) js_urls = [];\n",
              "\n",
              "    root._bokeh_onload_callbacks.push(callback);\n",
              "    if (root._bokeh_is_loading > 0) {\n",
              "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
              "      return null;\n",
              "    }\n",
              "    if (js_urls == null || js_urls.length === 0) {\n",
              "      run_callbacks();\n",
              "      return null;\n",
              "    }\n",
              "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
              "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
              "\n",
              "    function on_load() {\n",
              "      root._bokeh_is_loading--;\n",
              "      if (root._bokeh_is_loading === 0) {\n",
              "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
              "        run_callbacks()\n",
              "      }\n",
              "    }\n",
              "\n",
              "    function on_error(url) {\n",
              "      console.error(\"failed to load \" + url);\n",
              "    }\n",
              "\n",
              "    for (let i = 0; i < css_urls.length; i++) {\n",
              "      const url = css_urls[i];\n",
              "      const element = document.createElement(\"link\");\n",
              "      element.onload = on_load;\n",
              "      element.onerror = on_error.bind(null, url);\n",
              "      element.rel = \"stylesheet\";\n",
              "      element.type = \"text/css\";\n",
              "      element.href = url;\n",
              "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
              "      document.body.appendChild(element);\n",
              "    }\n",
              "\n",
              "    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\": \"dM3QQsP+wXdHg42wTqW85BjZQdLNNIXqlPw/BgKoExPmTG7ZLML4EGqLMfqHT6ON\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\": \"8x57I4YuIfu8XyZfFo0XVr2WAT8EK4rh/uDe3wF7YuW2FNUSNEpJbsPaB1nJ2fz2\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\": \"3QTqdz9LyAm2i0sG5XTePsHec3UHWwVsrOL68SYRoAXsafvfAyqtQ+h440+qIBhS\"};\n",
              "\n",
              "    for (let i = 0; i < js_urls.length; i++) {\n",
              "      const url = js_urls[i];\n",
              "      const element = document.createElement('script');\n",
              "      element.onload = on_load;\n",
              "      element.onerror = on_error.bind(null, url);\n",
              "      element.async = false;\n",
              "      element.src = url;\n",
              "      if (url in hashes) {\n",
              "        element.crossOrigin = \"anonymous\";\n",
              "        element.integrity = \"sha384-\" + hashes[url];\n",
              "      }\n",
              "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
              "      document.head.appendChild(element);\n",
              "    }\n",
              "  };\n",
              "\n",
              "  function inject_raw_css(css) {\n",
              "    const element = document.createElement(\"style\");\n",
              "    element.appendChild(document.createTextNode(css));\n",
              "    document.body.appendChild(element);\n",
              "  }\n",
              "\n",
              "  \n",
              "  var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\"];\n",
              "  var css_urls = [];\n",
              "  \n",
              "\n",
              "  var inline_js = [\n",
              "    function(Bokeh) {\n",
              "      Bokeh.set_log_level(\"info\");\n",
              "    },\n",
              "    function(Bokeh) {\n",
              "    \n",
              "    \n",
              "    }\n",
              "  ];\n",
              "\n",
              "  function run_inline_js() {\n",
              "    \n",
              "    if (root.Bokeh !== undefined || force === true) {\n",
              "      \n",
              "    for (var i = 0; i < inline_js.length; i++) {\n",
              "      inline_js[i].call(root, root.Bokeh);\n",
              "    }\n",
              "    } else if (Date.now() < root._bokeh_timeout) {\n",
              "      setTimeout(run_inline_js, 100);\n",
              "    } else if (!root._bokeh_failed_load) {\n",
              "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
              "      root._bokeh_failed_load = true;\n",
              "    } else if (force !== true) {\n",
              "      var cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
              "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
              "    }\n",
              "\n",
              "  }\n",
              "\n",
              "  if (root._bokeh_is_loading === 0) {\n",
              "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
              "    run_inline_js();\n",
              "  } else {\n",
              "    load_libs(css_urls, js_urls, function() {\n",
              "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
              "      run_inline_js();\n",
              "    });\n",
              "  }\n",
              "}(window));"
            ],
            "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  var force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n  \n\n  \n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  var NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    var el = document.getElementById(null);\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\": \"dM3QQsP+wXdHg42wTqW85BjZQdLNNIXqlPw/BgKoExPmTG7ZLML4EGqLMfqHT6ON\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\": \"8x57I4YuIfu8XyZfFo0XVr2WAT8EK4rh/uDe3wF7YuW2FNUSNEpJbsPaB1nJ2fz2\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\": \"3QTqdz9LyAm2i0sG5XTePsHec3UHWwVsrOL68SYRoAXsafvfAyqtQ+h440+qIBhS\"};\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      if (url in hashes) {\n        element.crossOrigin = \"anonymous\";\n        element.integrity = \"sha384-\" + hashes[url];\n      }\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  \n  var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\"];\n  var css_urls = [];\n  \n\n  var inline_js = [\n    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\n    function(Bokeh) {\n    \n    \n    }\n  ];\n\n  function run_inline_js() {\n    \n    if (root.Bokeh !== undefined || force === true) {\n      \n    for (var i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      var cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
          },
          "metadata": {}
        },
        {
          "output_type": "display_data",
          "data": {
            "text/html": [
              "\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "  <div class=\"bk-root\" id=\"159dba9c-8970-4c69-b948-9a16ea6d96fa\" data-root-id=\"2302\"></div>\n"
            ]
          },
          "metadata": {}
        },
        {
          "output_type": "display_data",
          "data": {
            "application/javascript": [
              "(function(root) {\n",
              "  function embed_document(root) {\n",
              "    \n",
              "  var docs_json = 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              "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
              "\n",
              "  }\n",
              "  if (root.Bokeh !== undefined) {\n",
              "    embed_document(root);\n",
              "  } else {\n",
              "    var attempts = 0;\n",
              "    var timer = setInterval(function(root) {\n",
              "      if (root.Bokeh !== undefined) {\n",
              "        clearInterval(timer);\n",
              "        embed_document(root);\n",
              "      } else {\n",
              "        attempts++;\n",
              "        if (attempts > 100) {\n",
              "          clearInterval(timer);\n",
              "          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n",
              "        }\n",
              "      }\n",
              "    }, 10, root)\n",
              "  }\n",
              "})(window);"
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