Untitled3.ipynb

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      "name": "Untitled3.ipynb",
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      "authorship_tag": "ABX9TyMQ4T5CvufR8jjlJjIhJzw2",
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      "name": "python3",
      "display_name": "Python 3"
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  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
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      "source": [
        "<a href=\"https://colab.research.google.com/github/ghenwafkh/miniproject/blob/master/Untitled3.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
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    {
      "cell_type": "markdown",
      "metadata": {
        "id": "xjcaxNDzIrnS",
        "colab_type": "text"
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      "source": [
        "\n",
        "2.0 Notebook 2: Exploratory Data Analysis\n",
        "Now that we have a good intuitive sense of the data, Next step involves taking a closer look at attributes and data values. In this section, I am getting familiar with the data, which will provide useful knowledge for data pre-processing."
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "4M4PDuHCI5Bj",
        "colab_type": "text"
      },
      "source": [
        "\n",
        "2.1 Descriptive statistics:\n",
        "Summary statistics are measurements meant to describe data. In the field of descriptive statistics, there are many summary measurements)"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "nlQAoPiPI-n-",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 72
        },
        "outputId": "d2469d8f-4efe-428f-869a-4791072c0634"
      },
      "source": [
        "import matplotlib.pyplot as plt\n",
        "\n",
        "#Load libraries for data processing\n",
        "import pandas as pd #data processing, CSV file I/O (e.g. pd.read_csv)\n",
        "import numpy as np\n",
        "from scipy.stats import norm\n",
        "import seaborn as sns # visualization\n",
        "\n",
        "\n",
        "plt.rcParams['figure.figsize'] = (15,8) \n",
        "plt.rcParams['axes.titlesize'] = 'large'"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/usr/local/lib/python3.6/dist-packages/statsmodels/tools/_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.\n",
            "  import pandas.util.testing as tm\n"
          ],
          "name": "stderr"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "I4430pOQJFuu",
        "colab_type": "code",
        "colab": {
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          "height": 144
        },
        "outputId": "c29d6de6-decc-4717-bcda-ccd4a613bc82"
      },
      "source": [
        "data = pd.read_csv('data/clean-data.csv', index_col=False)\n",
        "data.drop('Unnamed: 0',axis=1, inplace=True)\n",
        "data.head(2)"
      ],
      "execution_count": 4,
      "outputs": [
        {
          "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>diagnosis</th>\n",
              "      <th>radius_mean</th>\n",
              "      <th>texture_mean</th>\n",
              "      <th>perimeter_mean</th>\n",
              "      <th>area_mean</th>\n",
              "      <th>smoothness_mean</th>\n",
              "      <th>compactness_mean</th>\n",
              "      <th>concavity_mean</th>\n",
              "      <th>concave points_mean</th>\n",
              "      <th>symmetry_mean</th>\n",
              "      <th>fractal_dimension_mean</th>\n",
              "      <th>radius_se</th>\n",
              "      <th>texture_se</th>\n",
              "      <th>perimeter_se</th>\n",
              "      <th>area_se</th>\n",
              "      <th>smoothness_se</th>\n",
              "      <th>compactness_se</th>\n",
              "      <th>concavity_se</th>\n",
              "      <th>concave points_se</th>\n",
              "      <th>symmetry_se</th>\n",
              "      <th>fractal_dimension_se</th>\n",
              "      <th>radius_worst</th>\n",
              "      <th>texture_worst</th>\n",
              "      <th>perimeter_worst</th>\n",
              "      <th>area_worst</th>\n",
              "      <th>smoothness_worst</th>\n",
              "      <th>compactness_worst</th>\n",
              "      <th>concavity_worst</th>\n",
              "      <th>concave points_worst</th>\n",
              "      <th>symmetry_worst</th>\n",
              "      <th>fractal_dimension_worst</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>M</td>\n",
              "      <td>17.99</td>\n",
              "      <td>10.38</td>\n",
              "      <td>122.8</td>\n",
              "      <td>1001.0</td>\n",
              "      <td>0.11840</td>\n",
              "      <td>0.27760</td>\n",
              "      <td>0.3001</td>\n",
              "      <td>0.14710</td>\n",
              "      <td>0.2419</td>\n",
              "      <td>0.07871</td>\n",
              "      <td>1.0950</td>\n",
              "      <td>0.9053</td>\n",
              "      <td>8.589</td>\n",
              "      <td>153.40</td>\n",
              "      <td>0.006399</td>\n",
              "      <td>0.04904</td>\n",
              "      <td>0.05373</td>\n",
              "      <td>0.01587</td>\n",
              "      <td>0.03003</td>\n",
              "      <td>0.006193</td>\n",
              "      <td>25.38</td>\n",
              "      <td>17.33</td>\n",
              "      <td>184.6</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>0.1622</td>\n",
              "      <td>0.6656</td>\n",
              "      <td>0.7119</td>\n",
              "      <td>0.2654</td>\n",
              "      <td>0.4601</td>\n",
              "      <td>0.11890</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>M</td>\n",
              "      <td>20.57</td>\n",
              "      <td>17.77</td>\n",
              "      <td>132.9</td>\n",
              "      <td>1326.0</td>\n",
              "      <td>0.08474</td>\n",
              "      <td>0.07864</td>\n",
              "      <td>0.0869</td>\n",
              "      <td>0.07017</td>\n",
              "      <td>0.1812</td>\n",
              "      <td>0.05667</td>\n",
              "      <td>0.5435</td>\n",
              "      <td>0.7339</td>\n",
              "      <td>3.398</td>\n",
              "      <td>74.08</td>\n",
              "      <td>0.005225</td>\n",
              "      <td>0.01308</td>\n",
              "      <td>0.01860</td>\n",
              "      <td>0.01340</td>\n",
              "      <td>0.01389</td>\n",
              "      <td>0.003532</td>\n",
              "      <td>24.99</td>\n",
              "      <td>23.41</td>\n",
              "      <td>158.8</td>\n",
              "      <td>1956.0</td>\n",
              "      <td>0.1238</td>\n",
              "      <td>0.1866</td>\n",
              "      <td>0.2416</td>\n",
              "      <td>0.1860</td>\n",
              "      <td>0.2750</td>\n",
              "      <td>0.08902</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "  diagnosis  radius_mean  ...  symmetry_worst  fractal_dimension_worst\n",
              "0         M        17.99  ...          0.4601                  0.11890\n",
              "1         M        20.57  ...          0.2750                  0.08902\n",
              "\n",
              "[2 rows x 31 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 4
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "yYJrCl1vJJ4K",
        "colab_type": "code",
        "colab": {
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          "height": 324
        },
        "outputId": "1444e58d-2ff9-4c5f-d33d-86b239955e66"
      },
      "source": [
        "#basic descriptive statistics\n",
        "data.describe()"
      ],
      "execution_count": 5,
      "outputs": [
        {
          "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>radius_mean</th>\n",
              "      <th>texture_mean</th>\n",
              "      <th>perimeter_mean</th>\n",
              "      <th>area_mean</th>\n",
              "      <th>smoothness_mean</th>\n",
              "      <th>compactness_mean</th>\n",
              "      <th>concavity_mean</th>\n",
              "      <th>concave points_mean</th>\n",
              "      <th>symmetry_mean</th>\n",
              "      <th>fractal_dimension_mean</th>\n",
              "      <th>radius_se</th>\n",
              "      <th>texture_se</th>\n",
              "      <th>perimeter_se</th>\n",
              "      <th>area_se</th>\n",
              "      <th>smoothness_se</th>\n",
              "      <th>compactness_se</th>\n",
              "      <th>concavity_se</th>\n",
              "      <th>concave points_se</th>\n",
              "      <th>symmetry_se</th>\n",
              "      <th>fractal_dimension_se</th>\n",
              "      <th>radius_worst</th>\n",
              "      <th>texture_worst</th>\n",
              "      <th>perimeter_worst</th>\n",
              "      <th>area_worst</th>\n",
              "      <th>smoothness_worst</th>\n",
              "      <th>compactness_worst</th>\n",
              "      <th>concavity_worst</th>\n",
              "      <th>concave points_worst</th>\n",
              "      <th>symmetry_worst</th>\n",
              "      <th>fractal_dimension_worst</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>count</th>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "      <td>569.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>mean</th>\n",
              "      <td>14.127292</td>\n",
              "      <td>19.289649</td>\n",
              "      <td>91.969033</td>\n",
              "      <td>654.889104</td>\n",
              "      <td>0.096360</td>\n",
              "      <td>0.104341</td>\n",
              "      <td>0.088799</td>\n",
              "      <td>0.048919</td>\n",
              "      <td>0.181162</td>\n",
              "      <td>0.062798</td>\n",
              "      <td>0.405172</td>\n",
              "      <td>1.216853</td>\n",
              "      <td>2.866059</td>\n",
              "      <td>40.337079</td>\n",
              "      <td>0.007041</td>\n",
              "      <td>0.025478</td>\n",
              "      <td>0.031894</td>\n",
              "      <td>0.011796</td>\n",
              "      <td>0.020542</td>\n",
              "      <td>0.003795</td>\n",
              "      <td>16.269190</td>\n",
              "      <td>25.677223</td>\n",
              "      <td>107.261213</td>\n",
              "      <td>880.583128</td>\n",
              "      <td>0.132369</td>\n",
              "      <td>0.254265</td>\n",
              "      <td>0.272188</td>\n",
              "      <td>0.114606</td>\n",
              "      <td>0.290076</td>\n",
              "      <td>0.083946</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>std</th>\n",
              "      <td>3.524049</td>\n",
              "      <td>4.301036</td>\n",
              "      <td>24.298981</td>\n",
              "      <td>351.914129</td>\n",
              "      <td>0.014064</td>\n",
              "      <td>0.052813</td>\n",
              "      <td>0.079720</td>\n",
              "      <td>0.038803</td>\n",
              "      <td>0.027414</td>\n",
              "      <td>0.007060</td>\n",
              "      <td>0.277313</td>\n",
              "      <td>0.551648</td>\n",
              "      <td>2.021855</td>\n",
              "      <td>45.491006</td>\n",
              "      <td>0.003003</td>\n",
              "      <td>0.017908</td>\n",
              "      <td>0.030186</td>\n",
              "      <td>0.006170</td>\n",
              "      <td>0.008266</td>\n",
              "      <td>0.002646</td>\n",
              "      <td>4.833242</td>\n",
              "      <td>6.146258</td>\n",
              "      <td>33.602542</td>\n",
              "      <td>569.356993</td>\n",
              "      <td>0.022832</td>\n",
              "      <td>0.157336</td>\n",
              "      <td>0.208624</td>\n",
              "      <td>0.065732</td>\n",
              "      <td>0.061867</td>\n",
              "      <td>0.018061</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>min</th>\n",
              "      <td>6.981000</td>\n",
              "      <td>9.710000</td>\n",
              "      <td>43.790000</td>\n",
              "      <td>143.500000</td>\n",
              "      <td>0.052630</td>\n",
              "      <td>0.019380</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.106000</td>\n",
              "      <td>0.049960</td>\n",
              "      <td>0.111500</td>\n",
              "      <td>0.360200</td>\n",
              "      <td>0.757000</td>\n",
              "      <td>6.802000</td>\n",
              "      <td>0.001713</td>\n",
              "      <td>0.002252</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.007882</td>\n",
              "      <td>0.000895</td>\n",
              "      <td>7.930000</td>\n",
              "      <td>12.020000</td>\n",
              "      <td>50.410000</td>\n",
              "      <td>185.200000</td>\n",
              "      <td>0.071170</td>\n",
              "      <td>0.027290</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.156500</td>\n",
              "      <td>0.055040</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>25%</th>\n",
              "      <td>11.700000</td>\n",
              "      <td>16.170000</td>\n",
              "      <td>75.170000</td>\n",
              "      <td>420.300000</td>\n",
              "      <td>0.086370</td>\n",
              "      <td>0.064920</td>\n",
              "      <td>0.029560</td>\n",
              "      <td>0.020310</td>\n",
              "      <td>0.161900</td>\n",
              "      <td>0.057700</td>\n",
              "      <td>0.232400</td>\n",
              "      <td>0.833900</td>\n",
              "      <td>1.606000</td>\n",
              "      <td>17.850000</td>\n",
              "      <td>0.005169</td>\n",
              "      <td>0.013080</td>\n",
              "      <td>0.015090</td>\n",
              "      <td>0.007638</td>\n",
              "      <td>0.015160</td>\n",
              "      <td>0.002248</td>\n",
              "      <td>13.010000</td>\n",
              "      <td>21.080000</td>\n",
              "      <td>84.110000</td>\n",
              "      <td>515.300000</td>\n",
              "      <td>0.116600</td>\n",
              "      <td>0.147200</td>\n",
              "      <td>0.114500</td>\n",
              "      <td>0.064930</td>\n",
              "      <td>0.250400</td>\n",
              "      <td>0.071460</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>50%</th>\n",
              "      <td>13.370000</td>\n",
              "      <td>18.840000</td>\n",
              "      <td>86.240000</td>\n",
              "      <td>551.100000</td>\n",
              "      <td>0.095870</td>\n",
              "      <td>0.092630</td>\n",
              "      <td>0.061540</td>\n",
              "      <td>0.033500</td>\n",
              "      <td>0.179200</td>\n",
              "      <td>0.061540</td>\n",
              "      <td>0.324200</td>\n",
              "      <td>1.108000</td>\n",
              "      <td>2.287000</td>\n",
              "      <td>24.530000</td>\n",
              "      <td>0.006380</td>\n",
              "      <td>0.020450</td>\n",
              "      <td>0.025890</td>\n",
              "      <td>0.010930</td>\n",
              "      <td>0.018730</td>\n",
              "      <td>0.003187</td>\n",
              "      <td>14.970000</td>\n",
              "      <td>25.410000</td>\n",
              "      <td>97.660000</td>\n",
              "      <td>686.500000</td>\n",
              "      <td>0.131300</td>\n",
              "      <td>0.211900</td>\n",
              "      <td>0.226700</td>\n",
              "      <td>0.099930</td>\n",
              "      <td>0.282200</td>\n",
              "      <td>0.080040</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>75%</th>\n",
              "      <td>15.780000</td>\n",
              "      <td>21.800000</td>\n",
              "      <td>104.100000</td>\n",
              "      <td>782.700000</td>\n",
              "      <td>0.105300</td>\n",
              "      <td>0.130400</td>\n",
              "      <td>0.130700</td>\n",
              "      <td>0.074000</td>\n",
              "      <td>0.195700</td>\n",
              "      <td>0.066120</td>\n",
              "      <td>0.478900</td>\n",
              "      <td>1.474000</td>\n",
              "      <td>3.357000</td>\n",
              "      <td>45.190000</td>\n",
              "      <td>0.008146</td>\n",
              "      <td>0.032450</td>\n",
              "      <td>0.042050</td>\n",
              "      <td>0.014710</td>\n",
              "      <td>0.023480</td>\n",
              "      <td>0.004558</td>\n",
              "      <td>18.790000</td>\n",
              "      <td>29.720000</td>\n",
              "      <td>125.400000</td>\n",
              "      <td>1084.000000</td>\n",
              "      <td>0.146000</td>\n",
              "      <td>0.339100</td>\n",
              "      <td>0.382900</td>\n",
              "      <td>0.161400</td>\n",
              "      <td>0.317900</td>\n",
              "      <td>0.092080</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>max</th>\n",
              "      <td>28.110000</td>\n",
              "      <td>39.280000</td>\n",
              "      <td>188.500000</td>\n",
              "      <td>2501.000000</td>\n",
              "      <td>0.163400</td>\n",
              "      <td>0.345400</td>\n",
              "      <td>0.426800</td>\n",
              "      <td>0.201200</td>\n",
              "      <td>0.304000</td>\n",
              "      <td>0.097440</td>\n",
              "      <td>2.873000</td>\n",
              "      <td>4.885000</td>\n",
              "      <td>21.980000</td>\n",
              "      <td>542.200000</td>\n",
              "      <td>0.031130</td>\n",
              "      <td>0.135400</td>\n",
              "      <td>0.396000</td>\n",
              "      <td>0.052790</td>\n",
              "      <td>0.078950</td>\n",
              "      <td>0.029840</td>\n",
              "      <td>36.040000</td>\n",
              "      <td>49.540000</td>\n",
              "      <td>251.200000</td>\n",
              "      <td>4254.000000</td>\n",
              "      <td>0.222600</td>\n",
              "      <td>1.058000</td>\n",
              "      <td>1.252000</td>\n",
              "      <td>0.291000</td>\n",
              "      <td>0.663800</td>\n",
              "      <td>0.207500</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "       radius_mean  texture_mean  ...  symmetry_worst  fractal_dimension_worst\n",
              "count   569.000000    569.000000  ...      569.000000               569.000000\n",
              "mean     14.127292     19.289649  ...        0.290076                 0.083946\n",
              "std       3.524049      4.301036  ...        0.061867                 0.018061\n",
              "min       6.981000      9.710000  ...        0.156500                 0.055040\n",
              "25%      11.700000     16.170000  ...        0.250400                 0.071460\n",
              "50%      13.370000     18.840000  ...        0.282200                 0.080040\n",
              "75%      15.780000     21.800000  ...        0.317900                 0.092080\n",
              "max      28.110000     39.280000  ...        0.663800                 0.207500\n",
              "\n",
              "[8 rows x 30 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "bSNKLy5TJUOJ",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 567
        },
        "outputId": "ea385215-f4a9-4251-976d-0709cee4c9b2"
      },
      "source": [
        "data.skew()"
      ],
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "radius_mean                0.942380\n",
              "texture_mean               0.650450\n",
              "perimeter_mean             0.990650\n",
              "area_mean                  1.645732\n",
              "smoothness_mean            0.456324\n",
              "compactness_mean           1.190123\n",
              "concavity_mean             1.401180\n",
              "concave points_mean        1.171180\n",
              "symmetry_mean              0.725609\n",
              "fractal_dimension_mean     1.304489\n",
              "radius_se                  3.088612\n",
              "texture_se                 1.646444\n",
              "perimeter_se               3.443615\n",
              "area_se                    5.447186\n",
              "smoothness_se              2.314450\n",
              "compactness_se             1.902221\n",
              "concavity_se               5.110463\n",
              "concave points_se          1.444678\n",
              "symmetry_se                2.195133\n",
              "fractal_dimension_se       3.923969\n",
              "radius_worst               1.103115\n",
              "texture_worst              0.498321\n",
              "perimeter_worst            1.128164\n",
              "area_worst                 1.859373\n",
              "smoothness_worst           0.415426\n",
              "compactness_worst          1.473555\n",
              "concavity_worst            1.150237\n",
              "concave points_worst       0.492616\n",
              "symmetry_worst             1.433928\n",
              "fractal_dimension_worst    1.662579\n",
              "dtype: float64"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 6
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "zcJ9cISBJd24",
        "colab_type": "text"
      },
      "source": [
        "The skew result show a positive (right) or negative (left) skew. Values closer to zero show less skew. From the graphs, we can see that radius_mean, perimeter_mean, area_mean, concavity_mean and concave_points_mean are useful in predicting cancer type due to the distinct grouping between malignant and benign cancer types in these features. We can also see that area_worst and perimeter_worst are also quite useful."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "AH0zczxkJf49",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 34
        },
        "outputId": "588da9fa-57f0-4a6b-d2f6-106d22c662dc"
      },
      "source": [
        "data.diagnosis.unique()"
      ],
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "array(['M', 'B'], dtype=object)"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 7
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "x6Z0d-Y6JrX-",
        "colab_type": "text"
      },
      "source": [
        "\n",
        "2.3 Unimodal Data Visualizations:\n",
        "One of the main goals of visualizing the data here is to observe which features are most helpful in predicting malignant or benign cancer. The other is to see general trends that may aid us in model selection and hyper parameter selection."
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "vcWk3TBhJ2kf",
        "colab_type": "text"
      },
      "source": [
        "\n",
        "2.3.1 Visualise distribution of data via histograms"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "G3_aSLfFKDf7",
        "colab_type": "text"
      },
      "source": [
        "Separate columns into smaller dataframes to perform visualization"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "iqfegKNAKEr4",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 423
        },
        "outputId": "6afcd2fd-def0-4eb9-9d36-cd0b23ac81f6"
      },
      "source": [
        "\n",
        "#Break up columns into groups, according to their suffix designation \n",
        "#(_mean, _se,\n",
        "# and __worst) to perform visualisation plots off. \n",
        "#Join the 'ID' and 'Diagnosis' back on\n",
        "data_id_diag=data.loc[:,[\"id\",\"diagnosis\"]]\n",
        "data_diag=data.loc[:,[\"diagnosis\"]]\n",
        "\n",
        "#For a merge + slice:\n",
        "data_mean=data.ix[:,1:11]\n",
        "#data_se=data.ix[:,11:22]\n",
        "#data_worst=data.ix[:,23:]\n",
        "\n",
        "#print(df_id_diag.columns)\n",
        "#print(data_mean.columns)\n",
        "#print(data_se.columns)\n",
        "#print(data_worst.columns)"
      ],
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "error",
          "ename": "KeyError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-10-e57bff1ba27d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;31m# and __worst) to perform visualisation plots off.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;31m#Join the 'ID' and 'Diagnosis' back on\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0mdata_id_diag\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"id\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\"diagnosis\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      7\u001b[0m \u001b[0mdata_diag\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"diagnosis\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      8\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m   1760\u001b[0m                 \u001b[0;32mexcept\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mKeyError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mIndexError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mAttributeError\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1761\u001b[0m                     \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1762\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getitem_tuple\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1763\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1764\u001b[0m             \u001b[0;31m# we by definition only have the 0th axis\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_getitem_tuple\u001b[0;34m(self, tup)\u001b[0m\n\u001b[1;32m   1287\u001b[0m                 \u001b[0;32mcontinue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1288\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1289\u001b[0;31m             \u001b[0mretval\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mretval\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getitem_axis\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1290\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1291\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mretval\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_getitem_axis\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m   1952\u001b[0m                     \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Cannot index with multidimensional key\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1953\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1954\u001b[0;31m                 \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getitem_iterable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0maxis\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1955\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1956\u001b[0m             \u001b[0;31m# nested tuple slicing\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_getitem_iterable\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m   1593\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1594\u001b[0m             \u001b[0;31m# A collection of keys\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1595\u001b[0;31m             \u001b[0mkeyarr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_listlike_indexer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mraise_missing\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1596\u001b[0m             return self.obj._reindex_with_indexers(\n\u001b[1;32m   1597\u001b[0m                 \u001b[0;34m{\u001b[0m\u001b[0maxis\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mkeyarr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mallow_dups\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_get_listlike_indexer\u001b[0;34m(self, key, axis, raise_missing)\u001b[0m\n\u001b[1;32m   1551\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1552\u001b[0m         self._validate_read_indexer(\n\u001b[0;32m-> 1553\u001b[0;31m             \u001b[0mkeyarr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mo\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_axis_number\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maxis\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mraise_missing\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mraise_missing\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1554\u001b[0m         )\n\u001b[1;32m   1555\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mkeyarr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_validate_read_indexer\u001b[0;34m(self, key, indexer, axis, raise_missing)\u001b[0m\n\u001b[1;32m   1653\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0max\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_categorical\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0max\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_interval\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1654\u001b[0m                 raise KeyError(\n\u001b[0;32m-> 1655\u001b[0;31m                     \u001b[0;34m\"Passing list-likes to .loc or [] with any missing labels \"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1656\u001b[0m                     \u001b[0;34m\"is no longer supported, see \"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1657\u001b[0m                     \u001b[0;34m\"https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike\"\u001b[0m  \u001b[0;31m# noqa:E501\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;31mKeyError\u001b[0m: 'Passing list-likes to .loc or [] with any missing labels is no longer supported, see https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike'"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "IofUjsGDKVo3",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 185
        },
        "outputId": "90a73a59-4590-429a-a876-836395c64838"
      },
      "source": [
        "#Plot histograms of CUT1 variables\n",
        "hist_mean=data_mean.hist(bins=10, figsize=(15, 10),grid=False,)\n"
      ],
      "execution_count": 9,
      "outputs": [
        {
          "output_type": "error",
          "ename": "NameError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-9-008bb0547afc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m#Plot histograms of CUT1 variables\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mhist_mean\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdata_mean\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbins\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfigsize\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m15\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m10\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mgrid\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m: name 'data_mean' is not defined"
          ]
        }
      ]
    }
  ]
}