Added Colab notebook

1 files changed, 756 insertions, 0 deletions

diff --git a/COVID_19.ipynb b/COVID_19.ipynb
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+{
+  "nbformat": 4,
+  "nbformat_minor": 0,
+  "metadata": {
+    "colab": {
+      "name": "COVID-19.ipynb",
+      "provenance": [],
+      "collapsed_sections": []
+    },
+    "kernelspec": {
+      "name": "ir",
+      "display_name": "R"
+    }
+  },
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "5QHd73zDF7AQ",
+        "colab_type": "text"
+      },
+      "source": [
+        "# Possible Drugs for Combating COVID-19\n",
+        "\n",
+        "The base code is a fork of Tinka Vidovic's submission for Sage Health Competition"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "ZbxnissApuJx",
+        "colab_type": "text"
+      },
+      "source": [
+        "## Dependencies\n",
+        "\n",
+        "To access the Connectivity Map Data, we need to install the PharmacoGx library"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "Jw7YDVZhCq1R",
+        "colab_type": "code",
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 68
+        },
+        "outputId": "efb69b26-6403-480f-e88c-02c1ffafdbf5"
+      },
+      "source": [
+        "if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n",
+        "    install.packages(\"BiocManager\")"
+      ],
+      "execution_count": 1,
+      "outputs": [
+        {
+          "output_type": "stream",
+          "text": [
+            "Installing package into ‘/usr/local/lib/R/site-library’\n",
+            "(as ‘lib’ is unspecified)\n",
+            "\n"
+          ],
+          "name": "stderr"
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "mfQEYHamDD3j",
+        "colab_type": "code",
+        "outputId": "7ad00184-2a5a-4bd9-9f5f-6755863ab9f9",
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 241
+        }
+      },
+      "source": [
+        "BiocManager::install(\"PharmacoGx\")"
+      ],
+      "execution_count": 2,
+      "outputs": [
+        {
+          "output_type": "stream",
+          "text": [
+            "Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)\n",
+            "\n",
+            "Installing package(s) 'BiocVersion', 'PharmacoGx'\n",
+            "\n",
+            "also installing the dependencies ‘formatR’, ‘lambda.r’, ‘futile.options’, ‘futile.logger’, ‘snow’, ‘gtools’, ‘gdata’, ‘slam’, ‘sets’, ‘limma’, ‘data.table’, ‘BiocParallel’, ‘gridExtra’, ‘fastmatch’, ‘RANN’, ‘NISTunits’, ‘pracma’, ‘maps’, ‘BiocGenerics’, ‘gplots’, ‘igraph’, ‘relations’, ‘marray’, ‘fgsea’, ‘shinyjs’, ‘shinydashboard’, ‘visNetwork’, ‘celestial’, ‘plotrix’, ‘sm’, ‘mapproj’, ‘bitops’, ‘SnowballC’, ‘Biobase’, ‘piano’, ‘magicaxis’, ‘caTools’, ‘downloader’, ‘lsa’\n",
+            "\n",
+            "\n",
+            "Old packages: 'broom', 'covr', 'crosstalk', 'curl', 'dplyr', 'farver',\n",
+            "  'forcats', 'fs', 'ggplot2', 'glue', 'lifecycle', 'plyr', 'processx', 'rlang',\n",
+            "  'roxygen2', 'rprojroot', 'shiny', 'testthat', 'vctrs', 'xfun', 'xml2',\n",
+            "  'xtable', 'foreign', 'nlme', 'survival'\n",
+            "\n"
+          ],
+          "name": "stderr"
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "GzheUFgYDRdI",
+        "colab_type": "code",
+        "outputId": "53c655a6-3581-49bb-9791-4844256fb89d",
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 119
+        }
+      },
+      "source": [
+        "library(PharmacoGx)"
+      ],
+      "execution_count": 3,
+      "outputs": [
+        {
+          "output_type": "stream",
+          "text": [
+            "Warning message:\n",
+            "“no DISPLAY variable so Tk is not available”\n",
+            "Registered S3 method overwritten by 'ggplot2':\n",
+            "  method        from\n",
+            "  print.element sets\n",
+            "\n"
+          ],
+          "name": "stderr"
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "dPXPIiVjDZPd",
+        "colab_type": "code",
+        "outputId": "0063c9e9-34ff-4f7a-d8ea-e2c3f3fd68c8",
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 516
+        }
+      },
+      "source": [
+        "availablePSets()"
+      ],
+      "execution_count": 4,
+      "outputs": [
+        {
+          "output_type": "display_data",
+          "data": {
+            "text/plain": [
+              "                PSet.Name       Dataset.Type Available.Molecular.Profiles\n",
+              "CCLE_2013       CCLE_2013       sensitivity  rna/mutation                \n",
+              "CCLE            CCLE            sensitivity  rna/rnaseq/mutation/cnv     \n",
+              "GDSC_2013       GDSC_2013       sensitivity  rna/mutation                \n",
+              "GDSC            GDSC            sensitivity  rna/rna2/mutation/fusion/cnv\n",
+              "GDSC1000        GDSC1000        sensitivity  rna                         \n",
+              "gCSI            gCSI            sensitivity  rnaseq/cnv                  \n",
+              "FIMM            FIMM            sensitivity                              \n",
+              "CTRPv2          CTRPv2          sensitivity                              \n",
+              "CMAP            CMAP            perturbation rna                         \n",
+              "L1000_compounds L1000_compounds perturbation rna                         \n",
+              "L1000_genetic   L1000_genetic   perturbation rna                         \n",
+              "                Date.Updated            \n",
+              "CCLE_2013       Tue Sep 15 18:50:07 2015\n",
+              "CCLE            Thu Dec 10 18:17:14 2015\n",
+              "GDSC_2013       Mon Oct  5 16:07:54 2015\n",
+              "GDSC            Wed Dec 30 10:44:21 2015\n",
+              "GDSC1000        Thu Aug 25 11:13:00 2016\n",
+              "gCSI            Mon Jun 13 18:50:12 2016\n",
+              "FIMM            Mon Oct 3 17:14:00 2016 \n",
+              "CTRPv2          Thu Aug 25 11:15:00 2016\n",
+              "CMAP            Mon Sep 21 02:38:45 2015\n",
+              "L1000_compounds Mon Jan 25 12:51:00 2016\n",
+              "L1000_genetic   Mon Jan 25 12:51:00 2016\n",
+              "                URL                                                                                 \n",
+              "CCLE_2013       https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE_Nature2013.RData\n",
+              "CCLE            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData           \n",
+              "GDSC_2013       https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP_Nature2013.RData \n",
+              "GDSC            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData           \n",
+              "GDSC1000        https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData       \n",
+              "gCSI            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData           \n",
+              "FIMM            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData           \n",
+              "CTRPv2          https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData         \n",
+              "CMAP            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData           \n",
+              "L1000_compounds https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_compounds.RData\n",
+              "L1000_genetic   https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_genetic.RData  "
+            ],
+            "text/latex": "A data.frame: 11 × 5\n\\begin{tabular}{r|lllll}\n  & PSet.Name & Dataset.Type & Available.Molecular.Profiles & Date.Updated & URL\\\\\n  & <fct> & <fct> & <fct> & <fct> & <fct>\\\\\n\\hline\n\tCCLE\\_2013 & CCLE\\_2013       & sensitivity  & rna/mutation                 & Tue Sep 15 18:50:07 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE\\_Nature2013.RData\\\\\n\tCCLE & CCLE            & sensitivity  & rna/rnaseq/mutation/cnv      & Thu Dec 10 18:17:14 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData           \\\\\n\tGDSC\\_2013 & GDSC\\_2013       & sensitivity  & rna/mutation                 & Mon Oct  5 16:07:54 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP\\_Nature2013.RData \\\\\n\tGDSC & GDSC            & sensitivity  & rna/rna2/mutation/fusion/cnv & Wed Dec 30 10:44:21 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData           \\\\\n\tGDSC1000 & GDSC1000        & sensitivity  & rna                          & Thu Aug 25 11:13:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData       \\\\\n\tgCSI & gCSI            & sensitivity  & rnaseq/cnv                   & Mon Jun 13 18:50:12 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData           \\\\\n\tFIMM & FIMM            & sensitivity  &                              & Mon Oct 3 17:14:00 2016  & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData           \\\\\n\tCTRPv2 & CTRPv2          & sensitivity  &                              & Thu Aug 25 11:15:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData         \\\\\n\tCMAP & CMAP            & perturbation & rna                          & Mon Sep 21 02:38:45 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData           \\\\\n\tL1000\\_compounds & L1000\\_compounds & perturbation & rna                          & Mon Jan 25 12:51:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000\\_compounds.RData\\\\\n\tL1000\\_genetic & L1000\\_genetic   & perturbation & rna                          & Mon Jan 25 12:51:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000\\_genetic.RData  \\\\\n\\end{tabular}\n",
+            "text/markdown": "\nA data.frame: 11 × 5\n\n| <!--/--> | PSet.Name &lt;fct&gt; | Dataset.Type &lt;fct&gt; | Available.Molecular.Profiles &lt;fct&gt; | Date.Updated &lt;fct&gt; | URL &lt;fct&gt; |\n|---|---|---|---|---|---|\n| CCLE_2013 | CCLE_2013       | sensitivity  | rna/mutation                 | Tue Sep 15 18:50:07 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE_Nature2013.RData |\n| CCLE | CCLE            | sensitivity  | rna/rnaseq/mutation/cnv      | Thu Dec 10 18:17:14 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData            |\n| GDSC_2013 | GDSC_2013       | sensitivity  | rna/mutation                 | Mon Oct  5 16:07:54 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP_Nature2013.RData  |\n| GDSC | GDSC            | sensitivity  | rna/rna2/mutation/fusion/cnv | Wed Dec 30 10:44:21 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData            |\n| GDSC1000 | GDSC1000        | sensitivity  | rna                          | Thu Aug 25 11:13:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData        |\n| gCSI | gCSI            | sensitivity  | rnaseq/cnv                   | Mon Jun 13 18:50:12 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData            |\n| FIMM | FIMM            | sensitivity  | <!----> | Mon Oct 3 17:14:00 2016  | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData            |\n| CTRPv2 | CTRPv2          | sensitivity  | <!----> | Thu Aug 25 11:15:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData          |\n| CMAP | CMAP            | perturbation | rna                          | Mon Sep 21 02:38:45 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData            |\n| L1000_compounds | L1000_compounds | perturbation | rna                          | Mon Jan 25 12:51:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_compounds.RData |\n| L1000_genetic | L1000_genetic   | perturbation | rna                          | Mon Jan 25 12:51:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_genetic.RData   |\n\n",
+            "text/html": [
+              "<table>\n",
+              "<caption>A data.frame: 11 × 5</caption>\n",
+              "<thead>\n",
+              "\t<tr><th></th><th scope=col>PSet.Name</th><th scope=col>Dataset.Type</th><th scope=col>Available.Molecular.Profiles</th><th scope=col>Date.Updated</th><th scope=col>URL</th></tr>\n",
+              "\t<tr><th></th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th></tr>\n",
+              "</thead>\n",
+              "<tbody>\n",
+              "\t<tr><th scope=row>CCLE_2013</th><td>CCLE_2013      </td><td>sensitivity </td><td>rna/mutation                </td><td>Tue Sep 15 18:50:07 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE_Nature2013.RData</td></tr>\n",
+              "\t<tr><th scope=row>CCLE</th><td>CCLE           </td><td>sensitivity </td><td>rna/rnaseq/mutation/cnv     </td><td>Thu Dec 10 18:17:14 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData           </td></tr>\n",
+              "\t<tr><th scope=row>GDSC_2013</th><td>GDSC_2013      </td><td>sensitivity </td><td>rna/mutation                </td><td>Mon Oct  5 16:07:54 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP_Nature2013.RData </td></tr>\n",
+              "\t<tr><th scope=row>GDSC</th><td>GDSC           </td><td>sensitivity </td><td>rna/rna2/mutation/fusion/cnv</td><td>Wed Dec 30 10:44:21 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData           </td></tr>\n",
+              "\t<tr><th scope=row>GDSC1000</th><td>GDSC1000       </td><td>sensitivity </td><td>rna                         </td><td>Thu Aug 25 11:13:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData       </td></tr>\n",
+              "\t<tr><th scope=row>gCSI</th><td>gCSI           </td><td>sensitivity </td><td>rnaseq/cnv                  </td><td>Mon Jun 13 18:50:12 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData           </td></tr>\n",
+              "\t<tr><th scope=row>FIMM</th><td>FIMM           </td><td>sensitivity </td><td>                            </td><td>Mon Oct 3 17:14:00 2016 </td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData           </td></tr>\n",
+              "\t<tr><th scope=row>CTRPv2</th><td>CTRPv2         </td><td>sensitivity </td><td>                            </td><td>Thu Aug 25 11:15:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData         </td></tr>\n",
+              "\t<tr><th scope=row>CMAP</th><td>CMAP           </td><td>perturbation</td><td>rna                         </td><td>Mon Sep 21 02:38:45 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData           </td></tr>\n",
+              "\t<tr><th scope=row>L1000_compounds</th><td>L1000_compounds</td><td>perturbation</td><td>rna                         </td><td>Mon Jan 25 12:51:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_compounds.RData</td></tr>\n",
+              "\t<tr><th scope=row>L1000_genetic</th><td>L1000_genetic  </td><td>perturbation</td><td>rna                         </td><td>Mon Jan 25 12:51:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_genetic.RData  </td></tr>\n",
+              "</tbody>\n",
+              "</table>\n"
+            ]
+          },
+          "metadata": {
+            "tags": []
+          }
+        }
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "Cv2ZRsi7BJ4I",
+        "colab_type": "text"
+      },
+      "source": [
+        "## Downloading Dataset"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "uwzHt0hdGPk7",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "drugPerturbation = downloadPertSig(\"CMAP\")"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "pMkDzmNTFvgW",
+        "colab_type": "text"
+      },
+      "source": [
+        "## SARS"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "XAqpzSUbHZqk",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "download.file(url = \"https://raw.githubusercontent.com/navanchauhan/COVID-19/master/icSARS_Cov_Day7_None_GSE50000.csv\", destfile = \"SARS.csv\", method = \"wget\")"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "shz9Xd-mHgqL",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "sars_genes = read.csv(\"SARS.csv\", header = T, stringsAsFactors=F)\n",
+        "rownames(sars_genes) = sars_genes$Feature\n",
+        "sars = sars_genes$Direction\n",
+        "names(sars) = sars_genes$Feature"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "Ske4-qlhIV95",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "result_SARS = apply(\n",
+        "  drugPerturbation[,,c(\"tstat\", \"fdr\")],\n",
+        "  2,\n",
+        "  function(x, sars){\n",
+        "    return(\n",
+        "      connectivityScore(\n",
+        "        x=x,\n",
+        "        y=sars,\n",
+        "        method=\"fgsea\",\n",
+        "        nperm=100\n",
+        "                      )\n",
+        "        )\n",
+        "                    },sars = sars\n",
+        "  )"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "C--r-iYCIYsl",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "rownames(result_SARS) = c(\"Connectivity\", \"P_value\")\n",
+        "result_SARS = t(result_SARS)"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "K1BfNGY2JBPI",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "p_value_sars = result_SARS[order((result_SARS[,2]),decreasing = F),]"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "fUrHWW-WJC-_",
+        "colab_type": "code",
+        "outputId": "924918ce-ac98-486b-8bf4-0c838da624e1",
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 1000
+        }
+      },
+      "source": [
+        "p_value_sars"
+      ],
+      "execution_count": 26,
+      "outputs": [
+        {
+          "output_type": "display_data",
+          "data": {
+            "text/plain": [
+              "                                        Connectivity P_value    \n",
+              "rifabutin                               -0.340380    0.003296745\n",
+              "prochlorperazine                        -0.360245    0.003331658\n",
+              "phenazopyridine                         -0.321425    0.003346158\n",
+              "promazine                               -0.338460    0.003356367\n",
+              "syrosingopine                           -0.318895    0.003397262\n",
+              "levomepromazine                         -0.329905    0.003426580\n",
+              "nicergoline                             -0.297975    0.003437066\n",
+              "vorinostat                              -0.378310    0.003475393\n",
+              "maprotiline                             -0.345995    0.003528251\n",
+              "GW-8510                                 -0.365775    0.003659742\n",
+              "pyrvinium                               -0.312920    0.003809205\n",
+              "norcyclobenzaprine                      -0.319960    0.003837280\n",
+              "trifluoperazine                         -0.375195    0.004118781\n",
+              "ampyrone                                -0.302000    0.004346651\n",
+              "raloxifene                              -0.301795    0.004923140\n",
+              "fluphenazine                            -0.351740    0.005123401\n",
+              "methotrexate                            -0.336405    0.006074034\n",
+              "trichostatin A                          -0.330245    0.006293210\n",
+              "valproic acid                           -0.376625    0.006502227\n",
+              "rescinnamine                            -0.323295    0.006625811\n",
+              "nortriptyline                           -0.346990    0.006697707\n",
+              "eucatropine                             -0.288555    0.007156083\n",
+              "sirolimus                               -0.361685    0.007393165\n",
+              "Prestwick-559                           -0.332285    0.008811770\n",
+              "4,5-dianilinophthalimide                -0.809330    0.008840897\n",
+              "phenoxybenzamine                        -0.338050    0.008959175\n",
+              "resveratrol                             -0.350465    0.009149784\n",
+              "lycorine                                 0.319895    0.009335550\n",
+              "lasalocid                               -0.287965    0.009401784\n",
+              "HC toxin                                -0.371125    0.009747133\n",
+              "⋮                                       ⋮            ⋮          \n",
+              "PF-00562151-00                          0            1          \n",
+              "pioglitazone                            0            1          \n",
+              "PF-00539745-00                          0            1          \n",
+              "valdecoxib                              0            1          \n",
+              "PF-00539758-00                          0            1          \n",
+              "orlistat                                0            1          \n",
+              "5707885                                 0            1          \n",
+              "C-75                                    0            1          \n",
+              "5155877                                 0            1          \n",
+              "dinoprostone                            0            1          \n",
+              "5194442                                 0            1          \n",
+              "AG-028671                               0            1          \n",
+              "6-bromoindirubin-3'-oxime               0            1          \n",
+              "Gly-His-Lys                             0            1          \n",
+              "STOCK1N-35696                           0            1          \n",
+              "STOCK1N-28457                           0            1          \n",
+              "H-89                                    0            1          \n",
+              "SB-202190                               0            1          \n",
+              "NS-398                                  0            1          \n",
+              "SB-203580                               0            1          \n",
+              "AH-6809                                 0            1          \n",
+              "alsterpaullone                          0            1          \n",
+              "SC-19220                                0            1          \n",
+              "0198306-0000                            0            1          \n",
+              "AR-A014418                              0            1          \n",
+              "semustine                               0            1          \n",
+              "CP-944629                               0            1          \n",
+              "irinotecan                              0            1          \n",
+              "BCB000039                               0            1          \n",
+              "11-deoxy-16,16-dimethylprostaglandin E2 0            1          "
+            ],
+            "text/latex": "A matrix: 1288 × 2 of type dbl\n\\begin{tabular}{r|ll}\n  & Connectivity & P\\_value\\\\\n\\hline\n\trifabutin & -0.340380 & 0.003296745\\\\\n\tprochlorperazine & -0.360245 & 0.003331658\\\\\n\tphenazopyridine & -0.321425 & 0.003346158\\\\\n\tpromazine & -0.338460 & 0.003356367\\\\\n\tsyrosingopine & -0.318895 & 0.003397262\\\\\n\tlevomepromazine & -0.329905 & 0.003426580\\\\\n\tnicergoline & -0.297975 & 0.003437066\\\\\n\tvorinostat & -0.378310 & 0.003475393\\\\\n\tmaprotiline & -0.345995 & 0.003528251\\\\\n\tGW-8510 & -0.365775 & 0.003659742\\\\\n\tpyrvinium & -0.312920 & 0.003809205\\\\\n\tnorcyclobenzaprine & -0.319960 & 0.003837280\\\\\n\ttrifluoperazine & -0.375195 & 0.004118781\\\\\n\tampyrone & -0.302000 & 0.004346651\\\\\n\traloxifene & -0.301795 & 0.004923140\\\\\n\tfluphenazine & -0.351740 & 0.005123401\\\\\n\tmethotrexate & -0.336405 & 0.006074034\\\\\n\ttrichostatin A & -0.330245 & 0.006293210\\\\\n\tvalproic acid & -0.376625 & 0.006502227\\\\\n\trescinnamine & -0.323295 & 0.006625811\\\\\n\tnortriptyline & -0.346990 & 0.006697707\\\\\n\teucatropine & -0.288555 & 0.007156083\\\\\n\tsirolimus & -0.361685 & 0.007393165\\\\\n\tPrestwick-559 & -0.332285 & 0.008811770\\\\\n\t4,5-dianilinophthalimide & -0.809330 & 0.008840897\\\\\n\tphenoxybenzamine & -0.338050 & 0.008959175\\\\\n\tresveratrol & -0.350465 & 0.009149784\\\\\n\tlycorine &  0.319895 & 0.009335550\\\\\n\tlasalocid & -0.287965 & 0.009401784\\\\\n\tHC toxin & -0.371125 & 0.009747133\\\\\n\t⋮ & ⋮ & ⋮\\\\\n\tPF-00562151-00 & 0 & 1\\\\\n\tpioglitazone & 0 & 1\\\\\n\tPF-00539745-00 & 0 & 1\\\\\n\tvaldecoxib & 0 & 1\\\\\n\tPF-00539758-00 & 0 & 1\\\\\n\torlistat & 0 & 1\\\\\n\t5707885 & 0 & 1\\\\\n\tC-75 & 0 & 1\\\\\n\t5155877 & 0 & 1\\\\\n\tdinoprostone & 0 & 1\\\\\n\t5194442 & 0 & 1\\\\\n\tAG-028671 & 0 & 1\\\\\n\t6-bromoindirubin-3'-oxime & 0 & 1\\\\\n\tGly-His-Lys & 0 & 1\\\\\n\tSTOCK1N-35696 & 0 & 1\\\\\n\tSTOCK1N-28457 & 0 & 1\\\\\n\tH-89 & 0 & 1\\\\\n\tSB-202190 & 0 & 1\\\\\n\tNS-398 & 0 & 1\\\\\n\tSB-203580 & 0 & 1\\\\\n\tAH-6809 & 0 & 1\\\\\n\talsterpaullone & 0 & 1\\\\\n\tSC-19220 & 0 & 1\\\\\n\t0198306-0000 & 0 & 1\\\\\n\tAR-A014418 & 0 & 1\\\\\n\tsemustine & 0 & 1\\\\\n\tCP-944629 & 0 & 1\\\\\n\tirinotecan & 0 & 1\\\\\n\tBCB000039 & 0 & 1\\\\\n\t11-deoxy-16,16-dimethylprostaglandin E2 & 0 & 1\\\\\n\\end{tabular}\n",
+            "text/markdown": "\nA matrix: 1288 × 2 of type dbl\n\n| <!--/--> | Connectivity | P_value |\n|---|---|---|\n| rifabutin | -0.340380 | 0.003296745 |\n| prochlorperazine | -0.360245 | 0.003331658 |\n| phenazopyridine | -0.321425 | 0.003346158 |\n| promazine | -0.338460 | 0.003356367 |\n| syrosingopine | -0.318895 | 0.003397262 |\n| levomepromazine | -0.329905 | 0.003426580 |\n| nicergoline | -0.297975 | 0.003437066 |\n| vorinostat | -0.378310 | 0.003475393 |\n| maprotiline | -0.345995 | 0.003528251 |\n| GW-8510 | -0.365775 | 0.003659742 |\n| pyrvinium | -0.312920 | 0.003809205 |\n| norcyclobenzaprine | -0.319960 | 0.003837280 |\n| trifluoperazine | -0.375195 | 0.004118781 |\n| ampyrone | -0.302000 | 0.004346651 |\n| raloxifene | -0.301795 | 0.004923140 |\n| fluphenazine | -0.351740 | 0.005123401 |\n| methotrexate | -0.336405 | 0.006074034 |\n| trichostatin A | -0.330245 | 0.006293210 |\n| valproic acid | -0.376625 | 0.006502227 |\n| rescinnamine | -0.323295 | 0.006625811 |\n| nortriptyline | -0.346990 | 0.006697707 |\n| eucatropine | -0.288555 | 0.007156083 |\n| sirolimus | -0.361685 | 0.007393165 |\n| Prestwick-559 | -0.332285 | 0.008811770 |\n| 4,5-dianilinophthalimide | -0.809330 | 0.008840897 |\n| phenoxybenzamine | -0.338050 | 0.008959175 |\n| resveratrol | -0.350465 | 0.009149784 |\n| lycorine |  0.319895 | 0.009335550 |\n| lasalocid | -0.287965 | 0.009401784 |\n| HC toxin | -0.371125 | 0.009747133 |\n| ⋮ | ⋮ | ⋮ |\n| PF-00562151-00 | 0 | 1 |\n| pioglitazone | 0 | 1 |\n| PF-00539745-00 | 0 | 1 |\n| valdecoxib | 0 | 1 |\n| PF-00539758-00 | 0 | 1 |\n| orlistat | 0 | 1 |\n| 5707885 | 0 | 1 |\n| C-75 | 0 | 1 |\n| 5155877 | 0 | 1 |\n| dinoprostone | 0 | 1 |\n| 5194442 | 0 | 1 |\n| AG-028671 | 0 | 1 |\n| 6-bromoindirubin-3'-oxime | 0 | 1 |\n| Gly-His-Lys | 0 | 1 |\n| STOCK1N-35696 | 0 | 1 |\n| STOCK1N-28457 | 0 | 1 |\n| H-89 | 0 | 1 |\n| SB-202190 | 0 | 1 |\n| NS-398 | 0 | 1 |\n| SB-203580 | 0 | 1 |\n| AH-6809 | 0 | 1 |\n| alsterpaullone | 0 | 1 |\n| SC-19220 | 0 | 1 |\n| 0198306-0000 | 0 | 1 |\n| AR-A014418 | 0 | 1 |\n| semustine | 0 | 1 |\n| CP-944629 | 0 | 1 |\n| irinotecan | 0 | 1 |\n| BCB000039 | 0 | 1 |\n| 11-deoxy-16,16-dimethylprostaglandin E2 | 0 | 1 |\n\n",
+            "text/html": [
+              "<table>\n",
+              "<caption>A matrix: 1288 × 2 of type dbl</caption>\n",
+              "<thead>\n",
+              "\t<tr><th></th><th scope=col>Connectivity</th><th scope=col>P_value</th></tr>\n",
+              "</thead>\n",
+              "<tbody>\n",
+              "\t<tr><th scope=row>rifabutin</th><td>-0.340380</td><td>0.003296745</td></tr>\n",
+              "\t<tr><th scope=row>prochlorperazine</th><td>-0.360245</td><td>0.003331658</td></tr>\n",
+              "\t<tr><th scope=row>phenazopyridine</th><td>-0.321425</td><td>0.003346158</td></tr>\n",
+              "\t<tr><th scope=row>promazine</th><td>-0.338460</td><td>0.003356367</td></tr>\n",
+              "\t<tr><th scope=row>syrosingopine</th><td>-0.318895</td><td>0.003397262</td></tr>\n",
+              "\t<tr><th scope=row>levomepromazine</th><td>-0.329905</td><td>0.003426580</td></tr>\n",
+              "\t<tr><th scope=row>nicergoline</th><td>-0.297975</td><td>0.003437066</td></tr>\n",
+              "\t<tr><th scope=row>vorinostat</th><td>-0.378310</td><td>0.003475393</td></tr>\n",
+              "\t<tr><th scope=row>maprotiline</th><td>-0.345995</td><td>0.003528251</td></tr>\n",
+              "\t<tr><th scope=row>GW-8510</th><td>-0.365775</td><td>0.003659742</td></tr>\n",
+              "\t<tr><th scope=row>pyrvinium</th><td>-0.312920</td><td>0.003809205</td></tr>\n",
+              "\t<tr><th scope=row>norcyclobenzaprine</th><td>-0.319960</td><td>0.003837280</td></tr>\n",
+              "\t<tr><th scope=row>trifluoperazine</th><td>-0.375195</td><td>0.004118781</td></tr>\n",
+              "\t<tr><th scope=row>ampyrone</th><td>-0.302000</td><td>0.004346651</td></tr>\n",
+              "\t<tr><th scope=row>raloxifene</th><td>-0.301795</td><td>0.004923140</td></tr>\n",
+              "\t<tr><th scope=row>fluphenazine</th><td>-0.351740</td><td>0.005123401</td></tr>\n",
+              "\t<tr><th scope=row>methotrexate</th><td>-0.336405</td><td>0.006074034</td></tr>\n",
+              "\t<tr><th scope=row>trichostatin A</th><td>-0.330245</td><td>0.006293210</td></tr>\n",
+              "\t<tr><th scope=row>valproic acid</th><td>-0.376625</td><td>0.006502227</td></tr>\n",
+              "\t<tr><th scope=row>rescinnamine</th><td>-0.323295</td><td>0.006625811</td></tr>\n",
+              "\t<tr><th scope=row>nortriptyline</th><td>-0.346990</td><td>0.006697707</td></tr>\n",
+              "\t<tr><th scope=row>eucatropine</th><td>-0.288555</td><td>0.007156083</td></tr>\n",
+              "\t<tr><th scope=row>sirolimus</th><td>-0.361685</td><td>0.007393165</td></tr>\n",
+              "\t<tr><th scope=row>Prestwick-559</th><td>-0.332285</td><td>0.008811770</td></tr>\n",
+              "\t<tr><th scope=row>4,5-dianilinophthalimide</th><td>-0.809330</td><td>0.008840897</td></tr>\n",
+              "\t<tr><th scope=row>phenoxybenzamine</th><td>-0.338050</td><td>0.008959175</td></tr>\n",
+              "\t<tr><th scope=row>resveratrol</th><td>-0.350465</td><td>0.009149784</td></tr>\n",
+              "\t<tr><th scope=row>lycorine</th><td> 0.319895</td><td>0.009335550</td></tr>\n",
+              "\t<tr><th scope=row>lasalocid</th><td>-0.287965</td><td>0.009401784</td></tr>\n",
+              "\t<tr><th scope=row>HC toxin</th><td>-0.371125</td><td>0.009747133</td></tr>\n",
+              "\t<tr><th scope=row>⋮</th><td>⋮</td><td>⋮</td></tr>\n",
+              "\t<tr><th scope=row>PF-00562151-00</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>pioglitazone</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>PF-00539745-00</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>valdecoxib</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>PF-00539758-00</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>orlistat</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>5707885</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>C-75</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>5155877</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>dinoprostone</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>5194442</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>AG-028671</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>6-bromoindirubin-3'-oxime</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>Gly-His-Lys</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>STOCK1N-35696</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>STOCK1N-28457</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>H-89</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>SB-202190</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>NS-398</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>SB-203580</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>AH-6809</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>alsterpaullone</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>SC-19220</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>0198306-0000</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>AR-A014418</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>semustine</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>CP-944629</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>irinotecan</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>BCB000039</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>11-deoxy-16,16-dimethylprostaglandin E2</th><td>0</td><td>1</td></tr>\n",
+              "</tbody>\n",
+              "</table>\n"
+            ]
+          },
+          "metadata": {
+            "tags": []
+          }
+        }
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "BbC58sKwFyUi",
+        "colab_type": "text"
+      },
+      "source": [
+        "## MERS"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "7oFv2xQVJEsj",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "download.file(url = \"https://raw.githubusercontent.com/navanchauhan/COVID-19/master/HCoV_EMC2012_24Hour_23631916_GSE45042.csv\", destfile = \"MERS.csv\", method = \"wget\")"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "r3iLjkycKou9",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "mers_genes = read.csv(\"MERS.csv\",stringsAsFactors = F, header = T, sep=\",\")\n",
+        "rownames(mers_genes) = mers_genes$Feature\n",
+        "mers = mers_genes$Direction\n",
+        "names(mers) = mers_genes$Feature"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "uKfv_vOjKtcf",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "result_MERS = apply(\n",
+        "  drugPerturbation[,,c(\"tstat\", \"fdr\")],\n",
+        "  2,\n",
+        "  function(x, mers){\n",
+        "    return(\n",
+        "      connectivityScore(\n",
+        "        x=x,\n",
+        "        y=mers,\n",
+        "        method=\"fgsea\",\n",
+        "        nperm=100\n",
+        "                      )\n",
+        "        )\n",
+        "                    }, mers = mers\n",
+        "  )"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "TJaum6BnKvAP",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "rownames(result_MERS) = c(\"Connectivity\", \"P_value\")\n",
+        "result_MERS = t(result_MERS)"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "KkYUjIqmKwcu",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "p_value_mers = result_MERS[order((result_MERS[,2]),decreasing = F),]"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "V9XdAqjaKyVa",
+        "colab_type": "code",
+        "outputId": "55a67f34-85a5-4bd1-f28e-7c2b83dbf003",
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 1000
+        }
+      },
+      "source": [
+        "p_value_mers"
+      ],
+      "execution_count": 35,
+      "outputs": [
+        {
+          "output_type": "display_data",
+          "data": {
+            "text/plain": [
+              "                                        Connectivity P_value    \n",
+              "levomepromazine                         -0.329905    0.003302104\n",
+              "valproic acid                           -0.376625    0.003346158\n",
+              "syrosingopine                           -0.318895    0.003356370\n",
+              "resveratrol                             -0.350465    0.003504892\n",
+              "eucatropine                             -0.288555    0.003504892\n",
+              "prochlorperazine                        -0.360245    0.003519621\n",
+              "rescinnamine                            -0.323295    0.003554838\n",
+              "norcyclobenzaprine                      -0.319960    0.003584323\n",
+              "maprotiline                             -0.345995    0.003606370\n",
+              "nortriptyline                           -0.346990    0.003643482\n",
+              "ampyrone                                -0.302000    0.003951350\n",
+              "fluphenazine                            -0.351740    0.004253396\n",
+              "trifluoperazine                         -0.375195    0.004397685\n",
+              "vorinostat                              -0.378310    0.006276333\n",
+              "antimycin A                             -0.282915    0.006291056\n",
+              "CP-690334-01                            -0.286560    0.006316860\n",
+              "phenazopyridine                         -0.321425    0.006486558\n",
+              "trichostatin A                          -0.330245    0.006587867\n",
+              "chlorpromazine                          -0.312550    0.006712225\n",
+              "lasalocid                               -0.287965    0.006791518\n",
+              "GW-8510                                 -0.365775    0.006879944\n",
+              "LY-294002                               -0.358135    0.007161588\n",
+              "lycorine                                 0.319895    0.007339762\n",
+              "raloxifene                              -0.301795    0.007994990\n",
+              "promazine                               -0.338460    0.008005639\n",
+              "thioridazine                            -0.338605    0.008009466\n",
+              "metixene                                -0.288785    0.008806100\n",
+              "rifabutin                               -0.340380    0.008823347\n",
+              "vigabatrin                               0.294850    0.009206287\n",
+              "Prestwick-559                           -0.332285    0.009270520\n",
+              "⋮                                       ⋮            ⋮          \n",
+              "PF-00562151-00                          0            1          \n",
+              "pioglitazone                            0            1          \n",
+              "PF-00539745-00                          0            1          \n",
+              "valdecoxib                              0            1          \n",
+              "PF-00539758-00                          0            1          \n",
+              "orlistat                                0            1          \n",
+              "5707885                                 0            1          \n",
+              "C-75                                    0            1          \n",
+              "5155877                                 0            1          \n",
+              "dinoprostone                            0            1          \n",
+              "5194442                                 0            1          \n",
+              "AG-028671                               0            1          \n",
+              "6-bromoindirubin-3'-oxime               0            1          \n",
+              "Gly-His-Lys                             0            1          \n",
+              "STOCK1N-35696                           0            1          \n",
+              "STOCK1N-28457                           0            1          \n",
+              "H-89                                    0            1          \n",
+              "SB-202190                               0            1          \n",
+              "NS-398                                  0            1          \n",
+              "SB-203580                               0            1          \n",
+              "AH-6809                                 0            1          \n",
+              "alsterpaullone                          0            1          \n",
+              "SC-19220                                0            1          \n",
+              "0198306-0000                            0            1          \n",
+              "AR-A014418                              0            1          \n",
+              "semustine                               0            1          \n",
+              "CP-944629                               0            1          \n",
+              "irinotecan                              0            1          \n",
+              "BCB000039                               0            1          \n",
+              "11-deoxy-16,16-dimethylprostaglandin E2 0            1          "
+            ],
+            "text/latex": "A matrix: 1288 × 2 of type dbl\n\\begin{tabular}{r|ll}\n  & Connectivity & P\\_value\\\\\n\\hline\n\tlevomepromazine & -0.329905 & 0.003302104\\\\\n\tvalproic acid & -0.376625 & 0.003346158\\\\\n\tsyrosingopine & -0.318895 & 0.003356370\\\\\n\tresveratrol & -0.350465 & 0.003504892\\\\\n\teucatropine & -0.288555 & 0.003504892\\\\\n\tprochlorperazine & -0.360245 & 0.003519621\\\\\n\trescinnamine & -0.323295 & 0.003554838\\\\\n\tnorcyclobenzaprine & -0.319960 & 0.003584323\\\\\n\tmaprotiline & -0.345995 & 0.003606370\\\\\n\tnortriptyline & -0.346990 & 0.003643482\\\\\n\tampyrone & -0.302000 & 0.003951350\\\\\n\tfluphenazine & -0.351740 & 0.004253396\\\\\n\ttrifluoperazine & -0.375195 & 0.004397685\\\\\n\tvorinostat & -0.378310 & 0.006276333\\\\\n\tantimycin A & -0.282915 & 0.006291056\\\\\n\tCP-690334-01 & -0.286560 & 0.006316860\\\\\n\tphenazopyridine & -0.321425 & 0.006486558\\\\\n\ttrichostatin A & -0.330245 & 0.006587867\\\\\n\tchlorpromazine & -0.312550 & 0.006712225\\\\\n\tlasalocid & -0.287965 & 0.006791518\\\\\n\tGW-8510 & -0.365775 & 0.006879944\\\\\n\tLY-294002 & -0.358135 & 0.007161588\\\\\n\tlycorine &  0.319895 & 0.007339762\\\\\n\traloxifene & -0.301795 & 0.007994990\\\\\n\tpromazine & -0.338460 & 0.008005639\\\\\n\tthioridazine & -0.338605 & 0.008009466\\\\\n\tmetixene & -0.288785 & 0.008806100\\\\\n\trifabutin & -0.340380 & 0.008823347\\\\\n\tvigabatrin &  0.294850 & 0.009206287\\\\\n\tPrestwick-559 & -0.332285 & 0.009270520\\\\\n\t⋮ & ⋮ & ⋮\\\\\n\tPF-00562151-00 & 0 & 1\\\\\n\tpioglitazone & 0 & 1\\\\\n\tPF-00539745-00 & 0 & 1\\\\\n\tvaldecoxib & 0 & 1\\\\\n\tPF-00539758-00 & 0 & 1\\\\\n\torlistat & 0 & 1\\\\\n\t5707885 & 0 & 1\\\\\n\tC-75 & 0 & 1\\\\\n\t5155877 & 0 & 1\\\\\n\tdinoprostone & 0 & 1\\\\\n\t5194442 & 0 & 1\\\\\n\tAG-028671 & 0 & 1\\\\\n\t6-bromoindirubin-3'-oxime & 0 & 1\\\\\n\tGly-His-Lys & 0 & 1\\\\\n\tSTOCK1N-35696 & 0 & 1\\\\\n\tSTOCK1N-28457 & 0 & 1\\\\\n\tH-89 & 0 & 1\\\\\n\tSB-202190 & 0 & 1\\\\\n\tNS-398 & 0 & 1\\\\\n\tSB-203580 & 0 & 1\\\\\n\tAH-6809 & 0 & 1\\\\\n\talsterpaullone & 0 & 1\\\\\n\tSC-19220 & 0 & 1\\\\\n\t0198306-0000 & 0 & 1\\\\\n\tAR-A014418 & 0 & 1\\\\\n\tsemustine & 0 & 1\\\\\n\tCP-944629 & 0 & 1\\\\\n\tirinotecan & 0 & 1\\\\\n\tBCB000039 & 0 & 1\\\\\n\t11-deoxy-16,16-dimethylprostaglandin E2 & 0 & 1\\\\\n\\end{tabular}\n",
+            "text/markdown": "\nA matrix: 1288 × 2 of type dbl\n\n| <!--/--> | Connectivity | P_value |\n|---|---|---|\n| levomepromazine | -0.329905 | 0.003302104 |\n| valproic acid | -0.376625 | 0.003346158 |\n| syrosingopine | -0.318895 | 0.003356370 |\n| resveratrol | -0.350465 | 0.003504892 |\n| eucatropine | -0.288555 | 0.003504892 |\n| prochlorperazine | -0.360245 | 0.003519621 |\n| rescinnamine | -0.323295 | 0.003554838 |\n| norcyclobenzaprine | -0.319960 | 0.003584323 |\n| maprotiline | -0.345995 | 0.003606370 |\n| nortriptyline | -0.346990 | 0.003643482 |\n| ampyrone | -0.302000 | 0.003951350 |\n| fluphenazine | -0.351740 | 0.004253396 |\n| trifluoperazine | -0.375195 | 0.004397685 |\n| vorinostat | -0.378310 | 0.006276333 |\n| antimycin A | -0.282915 | 0.006291056 |\n| CP-690334-01 | -0.286560 | 0.006316860 |\n| phenazopyridine | -0.321425 | 0.006486558 |\n| trichostatin A | -0.330245 | 0.006587867 |\n| chlorpromazine | -0.312550 | 0.006712225 |\n| lasalocid | -0.287965 | 0.006791518 |\n| GW-8510 | -0.365775 | 0.006879944 |\n| LY-294002 | -0.358135 | 0.007161588 |\n| lycorine |  0.319895 | 0.007339762 |\n| raloxifene | -0.301795 | 0.007994990 |\n| promazine | -0.338460 | 0.008005639 |\n| thioridazine | -0.338605 | 0.008009466 |\n| metixene | -0.288785 | 0.008806100 |\n| rifabutin | -0.340380 | 0.008823347 |\n| vigabatrin |  0.294850 | 0.009206287 |\n| Prestwick-559 | -0.332285 | 0.009270520 |\n| ⋮ | ⋮ | ⋮ |\n| PF-00562151-00 | 0 | 1 |\n| pioglitazone | 0 | 1 |\n| PF-00539745-00 | 0 | 1 |\n| valdecoxib | 0 | 1 |\n| PF-00539758-00 | 0 | 1 |\n| orlistat | 0 | 1 |\n| 5707885 | 0 | 1 |\n| C-75 | 0 | 1 |\n| 5155877 | 0 | 1 |\n| dinoprostone | 0 | 1 |\n| 5194442 | 0 | 1 |\n| AG-028671 | 0 | 1 |\n| 6-bromoindirubin-3'-oxime | 0 | 1 |\n| Gly-His-Lys | 0 | 1 |\n| STOCK1N-35696 | 0 | 1 |\n| STOCK1N-28457 | 0 | 1 |\n| H-89 | 0 | 1 |\n| SB-202190 | 0 | 1 |\n| NS-398 | 0 | 1 |\n| SB-203580 | 0 | 1 |\n| AH-6809 | 0 | 1 |\n| alsterpaullone | 0 | 1 |\n| SC-19220 | 0 | 1 |\n| 0198306-0000 | 0 | 1 |\n| AR-A014418 | 0 | 1 |\n| semustine | 0 | 1 |\n| CP-944629 | 0 | 1 |\n| irinotecan | 0 | 1 |\n| BCB000039 | 0 | 1 |\n| 11-deoxy-16,16-dimethylprostaglandin E2 | 0 | 1 |\n\n",
+            "text/html": [
+              "<table>\n",
+              "<caption>A matrix: 1288 × 2 of type dbl</caption>\n",
+              "<thead>\n",
+              "\t<tr><th></th><th scope=col>Connectivity</th><th scope=col>P_value</th></tr>\n",
+              "</thead>\n",
+              "<tbody>\n",
+              "\t<tr><th scope=row>levomepromazine</th><td>-0.329905</td><td>0.003302104</td></tr>\n",
+              "\t<tr><th scope=row>valproic acid</th><td>-0.376625</td><td>0.003346158</td></tr>\n",
+              "\t<tr><th scope=row>syrosingopine</th><td>-0.318895</td><td>0.003356370</td></tr>\n",
+              "\t<tr><th scope=row>resveratrol</th><td>-0.350465</td><td>0.003504892</td></tr>\n",
+              "\t<tr><th scope=row>eucatropine</th><td>-0.288555</td><td>0.003504892</td></tr>\n",
+              "\t<tr><th scope=row>prochlorperazine</th><td>-0.360245</td><td>0.003519621</td></tr>\n",
+              "\t<tr><th scope=row>rescinnamine</th><td>-0.323295</td><td>0.003554838</td></tr>\n",
+              "\t<tr><th scope=row>norcyclobenzaprine</th><td>-0.319960</td><td>0.003584323</td></tr>\n",
+              "\t<tr><th scope=row>maprotiline</th><td>-0.345995</td><td>0.003606370</td></tr>\n",
+              "\t<tr><th scope=row>nortriptyline</th><td>-0.346990</td><td>0.003643482</td></tr>\n",
+              "\t<tr><th scope=row>ampyrone</th><td>-0.302000</td><td>0.003951350</td></tr>\n",
+              "\t<tr><th scope=row>fluphenazine</th><td>-0.351740</td><td>0.004253396</td></tr>\n",
+              "\t<tr><th scope=row>trifluoperazine</th><td>-0.375195</td><td>0.004397685</td></tr>\n",
+              "\t<tr><th scope=row>vorinostat</th><td>-0.378310</td><td>0.006276333</td></tr>\n",
+              "\t<tr><th scope=row>antimycin A</th><td>-0.282915</td><td>0.006291056</td></tr>\n",
+              "\t<tr><th scope=row>CP-690334-01</th><td>-0.286560</td><td>0.006316860</td></tr>\n",
+              "\t<tr><th scope=row>phenazopyridine</th><td>-0.321425</td><td>0.006486558</td></tr>\n",
+              "\t<tr><th scope=row>trichostatin A</th><td>-0.330245</td><td>0.006587867</td></tr>\n",
+              "\t<tr><th scope=row>chlorpromazine</th><td>-0.312550</td><td>0.006712225</td></tr>\n",
+              "\t<tr><th scope=row>lasalocid</th><td>-0.287965</td><td>0.006791518</td></tr>\n",
+              "\t<tr><th scope=row>GW-8510</th><td>-0.365775</td><td>0.006879944</td></tr>\n",
+              "\t<tr><th scope=row>LY-294002</th><td>-0.358135</td><td>0.007161588</td></tr>\n",
+              "\t<tr><th scope=row>lycorine</th><td> 0.319895</td><td>0.007339762</td></tr>\n",
+              "\t<tr><th scope=row>raloxifene</th><td>-0.301795</td><td>0.007994990</td></tr>\n",
+              "\t<tr><th scope=row>promazine</th><td>-0.338460</td><td>0.008005639</td></tr>\n",
+              "\t<tr><th scope=row>thioridazine</th><td>-0.338605</td><td>0.008009466</td></tr>\n",
+              "\t<tr><th scope=row>metixene</th><td>-0.288785</td><td>0.008806100</td></tr>\n",
+              "\t<tr><th scope=row>rifabutin</th><td>-0.340380</td><td>0.008823347</td></tr>\n",
+              "\t<tr><th scope=row>vigabatrin</th><td> 0.294850</td><td>0.009206287</td></tr>\n",
+              "\t<tr><th scope=row>Prestwick-559</th><td>-0.332285</td><td>0.009270520</td></tr>\n",
+              "\t<tr><th scope=row>⋮</th><td>⋮</td><td>⋮</td></tr>\n",
+              "\t<tr><th scope=row>PF-00562151-00</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>pioglitazone</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>PF-00539745-00</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>valdecoxib</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>PF-00539758-00</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>orlistat</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>5707885</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>C-75</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>5155877</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>dinoprostone</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>5194442</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>AG-028671</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>6-bromoindirubin-3'-oxime</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>Gly-His-Lys</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>STOCK1N-35696</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>STOCK1N-28457</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>H-89</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>SB-202190</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>NS-398</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>SB-203580</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>AH-6809</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>alsterpaullone</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>SC-19220</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>0198306-0000</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>AR-A014418</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>semustine</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>CP-944629</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>irinotecan</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>BCB000039</th><td>0</td><td>1</td></tr>\n",
+              "\t<tr><th scope=row>11-deoxy-16,16-dimethylprostaglandin E2</th><td>0</td><td>1</td></tr>\n",
+              "</tbody>\n",
+              "</table>\n"
+            ]
+          },
+          "metadata": {
+            "tags": []
+          }
+        }
+      ]
+    }
+  ]
+}
\ No newline at end of file