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diff --git a/COVID_19.ipynb b/COVID_19.ipynb new file mode 100644 index 0000000..431cf4f --- /dev/null +++ b/COVID_19.ipynb @@ -0,0 +1,756 @@ +{ + "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 <fct> | Dataset.Type <fct> | Available.Molecular.Profiles <fct> | Date.Updated <fct> | URL <fct> |\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><fct></th><th scope=col><fct></th><th scope=col><fct></th><th scope=col><fct></th><th scope=col><fct></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": [] + } + } + ] + } + ] +}
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