tests/cookbook-quartet-species-tree.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Inferring species trees with *tetrad*\n",
    "\n",
    "When you install _ipyrad_ a number of analysis tools are installed as well. This includes the program __tetrad__, which applies the theory of phylogenetic invariants (see Lake 1987) to infer quartet trees based on a SNP alignment. It then uses the software wQMC to join the quartets into a species tree. This combined approach was first developed by Chifman and Kubatko (2015) in the software *SVDQuartets*. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Required software"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "## conda install ipyrad -c ipyrad\n",
    "## conda install toytree -c eaton-lab"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import ipyrad.analysis as ipa\n",
    "import ipyparallel as ipp\n",
    "import toytree"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Connect to a cluster"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "connected to 4 cores\n"
     ]
    }
   ],
   "source": [
    "## connect to a cluster\n",
    "ipyclient = ipp.Client()\n",
    "print(\"connected to {} cores\".format(len(ipyclient)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run tetrad"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading seq array [13 taxa x 14159 bp]\n",
      "max unlinked SNPs per quartet (nloci): 2777\n"
     ]
    }
   ],
   "source": [
    "## initiate a tetrad object\n",
    "tet = ipa.tetrad(\n",
    "    name=\"pedic-full\",\n",
    "    seqfile=\"analysis-ipyrad/pedic-full_outfiles/pedic-full.snps.phy\",\n",
    "    mapfile=\"analysis-ipyrad/pedic-full_outfiles/pedic-full.snps.map\",\n",
    "    nboots=100,\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "host compute node: [4 cores] on oud\n",
      "inferring 715 induced quartet trees\n",
      "[####################] 100%  initial tree | 0:00:06 |  \n",
      "[####################] 100%  boot 100     | 0:01:00 |  \n"
     ]
    }
   ],
   "source": [
    "## run tetrad on the cluster\n",
    "tet.run(ipyclient=ipyclient)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Plot the tree"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div class=\"toyplot\" id=\"tcfbca9efd36b498a8511760c3cbe960d\" style=\"text-align:center\"><svg class=\"toyplot-canvas-Canvas\" height=\"350.0px\" id=\"ta061e61770094567a96d1b31901e4424\" preserveAspectRatio=\"xMidYMid meet\" style=\"background-color:transparent;fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:Helvetica;font-size:12px;opacity:1.0;stroke:rgb(16.1%,15.3%,14.1%);stroke-opacity:1.0;stroke-width:1.0\" viewBox=\"0 0 350.0 350.0\" width=\"350.0px\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:toyplot=\"http://www.sandia.gov/toyplot\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"><g class=\"toyplot-coordinates-Cartesian\" id=\"t73ee24b8f6bf4a539134688310303177\"><clipPath id=\"t93cbdce5b26448aca2d67929bd9cd1c9\"><rect height=\"350.0\" width=\"350.0\" x=\"0.0\" y=\"0.0\"></rect></clipPath><g clip-path=\"url(#t93cbdce5b26448aca2d67929bd9cd1c9)\"><g class=\"toyplot-mark-Text\" id=\"t50e6813c08de449cb51ddd18d96cc2c8\"><g class=\"toyplot-Series\"><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,56.807866868381225)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">33588_przewalskii</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,76.506555723651019)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">32082_przewalskii</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,96.205244578920798)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">30686_cyathophylla</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,115.90393343419063)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">29154_superba</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,135.60262228946041)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">41954_cyathophylloides</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,155.30131114473022)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">41478_cyathophylloides</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,175.0)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">33413_thamno</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,194.69868885526981)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">30556_thamno</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,214.39737771053959)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">35236_rex</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,234.09606656580942)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">35855_rex</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,253.79475542107917)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">40578_rex</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,273.49344427634901)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">38362_rex</text></g><g class=\"toyplot-Datum\" transform=\"translate(215.02260149550079,293.19213313161879)\"><text style=\"fill:rgb(16.1%,15.3%,14.1%);fill-opacity:1.0;font-family:helvetica;font-size:12.0;font-weight:normal;opacity:1.0;stroke:none;vertical-align:baseline;white-space:pre\" x=\"15.0\" y=\"3.066\">39618_rex</text></g></g></g><g class=\"toyplot-mark-Graph\" id=\"t61b531b21e3b4dbfa81c115ea7e1ee7b\"><g class=\"toyplot-Edges\"><path d=\"M 50.0 129.446782022 L 50.0 66.657211296\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 50.0 66.657211296 L 187.51883458 66.657211296\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 50.0 129.446782022 L 50.0 125.753277862\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 50.0 125.753277862 L 160.015067664 125.753277862\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 50.0 129.446782022 L 50.0 195.929856909\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 50.0 195.929856909 L 77.5037669159 195.929856909\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 66.657211296 L 187.51883458 56.8078668684\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 56.8078668684 L 215.022601496 56.8078668684\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 66.657211296 L 187.51883458 76.5065557237\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 76.5065557237 L 215.022601496 76.5065557237\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 125.753277862 L 160.015067664 106.054589007\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 106.054589007 L 187.51883458 106.054589007\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 125.753277862 L 160.015067664 145.451966717\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 145.451966717 L 187.51883458 145.451966717\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 77.5037669159 195.929856909 L 77.5037669159 175.0\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 77.5037669159 175.0 L 215.022601496 175.0\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 77.5037669159 195.929856909 L 77.5037669159 216.859713817\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 77.5037669159 216.859713817 L 105.007533832 216.859713817\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 106.054589007 L 187.51883458 96.2052445789\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 96.2052445789 L 215.022601496 96.2052445789\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 106.054589007 L 187.51883458 115.903933434\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 115.903933434 L 215.022601496 115.903933434\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 145.451966717 L 187.51883458 135.602622289\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 135.602622289 L 215.022601496 135.602622289\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 145.451966717 L 187.51883458 155.301311145\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 155.301311145 L 215.022601496 155.301311145\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 105.007533832 216.859713817 L 105.007533832 194.698688855\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 105.007533832 194.698688855 L 215.022601496 194.698688855\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 105.007533832 216.859713817 L 105.007533832 239.02073878\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 105.007533832 239.02073878 L 132.511300748 239.02073878\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 132.511300748 239.02073878 L 132.511300748 214.397377711\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 132.511300748 214.397377711 L 215.022601496 214.397377711\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 132.511300748 239.02073878 L 132.511300748 263.644099849\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 132.511300748 263.644099849 L 160.015067664 263.644099849\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 263.644099849 L 160.015067664 243.945410993\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 243.945410993 L 187.51883458 243.945410993\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 263.644099849 L 160.015067664 283.342788704\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 160.015067664 283.342788704 L 187.51883458 283.342788704\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 243.945410993 L 187.51883458 234.096066566\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 234.096066566 L 215.022601496 234.096066566\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 243.945410993 L 187.51883458 253.794755421\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 253.794755421 L 215.022601496 253.794755421\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 283.342788704 L 187.51883458 273.493444276\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 273.493444276 L 215.022601496 273.493444276\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 283.342788704 L 187.51883458 293.192133132\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path><path d=\"M 187.51883458 293.192133132 L 215.022601496 293.192133132\" style=\"fill:none;stroke:rgb(16.1%,15.3%,14.1%);stroke-linecap:round;stroke-opacity:1.0;stroke-width:2\"></path></g><g class=\"toyplot-Vertices\"><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"50.0\" cy=\"129.44678202218859\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"50.0\" cy=\"66.657211296016129\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"66.657211296016129\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"50.0\" cy=\"125.7532778618255\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"125.7532778618255\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"50.0\" cy=\"195.92985690872419\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"77.503766915916799\" cy=\"195.92985690872419\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"66.657211296016129\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"56.807866868381225\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"56.807866868381225\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"76.506555723651019\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"76.506555723651019\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"125.7532778618255\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"106.05458900655572\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"106.05458900655572\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"145.4519667170953\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"145.4519667170953\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"77.503766915916799\" cy=\"195.92985690872419\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"77.503766915916799\" cy=\"175.0\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"175.0\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"77.503766915916799\" cy=\"216.8597138174483\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"105.0075338318336\" cy=\"216.8597138174483\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"106.05458900655572\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"96.205244578920798\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"96.205244578920798\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"115.90393343419063\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"115.90393343419063\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"145.4519667170953\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"135.60262228946041\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"135.60262228946041\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"155.30131114473022\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"155.30131114473022\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"105.0075338318336\" cy=\"216.8597138174483\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"105.0075338318336\" cy=\"194.69868885526981\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"194.69868885526981\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"105.0075338318336\" cy=\"239.02073877962684\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"132.5113007477504\" cy=\"239.02073877962684\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"132.5113007477504\" cy=\"239.02073877962684\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"132.5113007477504\" cy=\"214.39737771053959\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"214.39737771053959\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"132.5113007477504\" cy=\"263.64409984871406\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"263.64409984871406\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"263.64409984871406\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"243.94541099344428\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"243.94541099344428\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"160.0150676636672\" cy=\"283.3427887039839\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"283.3427887039839\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"243.94541099344428\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"234.09606656580942\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"234.09606656580942\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"253.79475542107917\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"253.79475542107917\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"283.3427887039839\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"273.49344427634901\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"273.49344427634901\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"187.518834579584\" cy=\"293.19213313161879\" r=\"0.0\"></circle></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:rgb(40%,76.1%,64.7%);stroke-opacity:1.0\"><circle cx=\"215.02260149550079\" cy=\"293.19213313161879\" r=\"0.0\"></circle></g></g></g><g class=\"toyplot-mark-Scatterplot\" id=\"t4f0ba7ba20e34ddb9bba73750915d55b\"><g class=\"toyplot-Series\"><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 1\n",
       "name: 1\n",
       "dist: 100\n",
       "support: 100</title><circle cx=\"187.518834579584\" cy=\"66.657211296016129\" r=\"11.0\"></circle><g transform=\"translate(187.518834579584,66.657211296016129)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-10.506\" y=\"3.7995\">100</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 2\n",
       "name: 2\n",
       "dist: 100\n",
       "support: 100</title><circle cx=\"160.0150676636672\" cy=\"125.7532778618255\" r=\"11.0\"></circle><g transform=\"translate(160.0150676636672,125.7532778618255)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-10.506\" y=\"3.7995\">100</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 3\n",
       "name: 3\n",
       "dist: 100\n",
       "support: 100</title><circle cx=\"187.518834579584\" cy=\"106.05458900655572\" r=\"11.0\"></circle><g transform=\"translate(187.518834579584,106.05458900655572)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-10.506\" y=\"3.7995\">100</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 4\n",
       "name: 4\n",
       "dist: 100\n",
       "support: 100</title><circle cx=\"187.518834579584\" cy=\"145.4519667170953\" r=\"11.0\"></circle><g transform=\"translate(187.518834579584,145.4519667170953)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-10.506\" y=\"3.7995\">100</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 5\n",
       "name: 5\n",
       "dist: 100\n",
       "support: 100</title><circle cx=\"77.503766915916799\" cy=\"195.92985690872419\" r=\"11.0\"></circle><g transform=\"translate(77.503766915916799,195.92985690872419)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-10.506\" y=\"3.7995\">100</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 6\n",
       "name: 6\n",
       "dist: 81\n",
       "support: 81</title><circle cx=\"105.0075338318336\" cy=\"216.8597138174483\" r=\"11.0\"></circle><g transform=\"translate(105.0075338318336,216.8597138174483)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-7.004\" y=\"3.7995\">81</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 7\n",
       "name: 7\n",
       "dist: 48\n",
       "support: 48</title><circle cx=\"132.5113007477504\" cy=\"239.02073877962684\" r=\"11.0\"></circle><g transform=\"translate(132.5113007477504,239.02073877962684)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-7.004\" y=\"3.7995\">48</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 8\n",
       "name: 8\n",
       "dist: 35\n",
       "support: 35</title><circle cx=\"160.0150676636672\" cy=\"263.64409984871406\" r=\"11.0\"></circle><g transform=\"translate(160.0150676636672,263.64409984871406)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-7.004\" y=\"3.7995\">35</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 9\n",
       "name: 9\n",
       "dist: 100\n",
       "support: 100</title><circle cx=\"187.518834579584\" cy=\"243.94541099344428\" r=\"11.0\"></circle><g transform=\"translate(187.518834579584,243.94541099344428)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-10.506\" y=\"3.7995\">100</text></g></g><g class=\"toyplot-Datum\" style=\"fill:rgb(40%,76.1%,64.7%);fill-opacity:1.0;opacity:1.0;stroke:none\"><title>idx: 10\n",
       "name: 10\n",
       "dist: 100\n",
       "support: 100</title><circle cx=\"187.518834579584\" cy=\"283.3427887039839\" r=\"11.0\"></circle><g transform=\"translate(187.518834579584,283.3427887039839)\"><text style=\"fill:rgb(14.9%,14.9%,14.9%);fill-opacity:1.0;font-family:helvetica;font-size:9.0;font-weight:normal;stroke:none;vertical-align:baseline;white-space:pre\" x=\"-10.506\" y=\"3.7995\">100</text></g></g></g></g></g></g></svg><div class=\"toyplot-behavior\"><script>(function()\n",
       "{\n",
       "var modules={};\n",
       "modules[\"toyplot/tables\"] = (function()\n",
       "    {\n",
       "        var tables = [];\n",
       "\n",
       "        var module = {};\n",
       "\n",
       "        module.store = function(owner, key, names, columns)\n",
       "        {\n",
       "            tables.push({owner: owner, key: key, names: names, columns: columns});\n",
       "        }\n",
       "\n",
       "        module.get_csv = function(owner, key)\n",
       "        {\n",
       "            var csv = \"\";\n",
       "            for(var i = 0; i != tables.length; ++i)\n",
       "            {\n",
       "                var table = tables[i];\n",
       "                if(table.owner != owner)\n",
       "                    continue;\n",
       "                if(table.key != key)\n",
       "                    continue;\n",
       "\n",
       "                csv += table.names.join(\",\") + \"\\n\";\n",
       "                for(var i = 0; i != table.columns[0].length; ++i)\n",
       "                {\n",
       "                  for(var j = 0; j != table.columns.length; ++j)\n",
       "                  {\n",
       "                    if(j)\n",
       "                      csv += \",\";\n",
       "                    csv += table.columns[j][i];\n",
       "                  }\n",
       "                  csv += \"\\n\";\n",
       "                }\n",
       "                return csv;\n",
       "            }\n",
       "        }\n",
       "\n",
       "        return module;\n",
       "    })();\n",
       "modules[\"toyplot/root/id\"] = \"tcfbca9efd36b498a8511760c3cbe960d\";\n",
       "modules[\"toyplot/root\"] = (function(root_id)\n",
       "    {\n",
       "        return document.querySelector(\"#\" + root_id);\n",
       "    })(modules[\"toyplot/root/id\"]);\n",
       "modules[\"toyplot/canvas/id\"] = \"ta061e61770094567a96d1b31901e4424\";\n",
       "modules[\"toyplot/canvas\"] = (function(canvas_id)\n",
       "    {\n",
       "        return document.querySelector(\"#\" + canvas_id);\n",
       "    })(modules[\"toyplot/canvas/id\"]);\n",
       "modules[\"toyplot/menus/context\"] = (function(root, canvas)\n",
       "    {\n",
       "        var wrapper = document.createElement(\"div\");\n",
       "        wrapper.innerHTML = \"<ul class='toyplot-context-menu' style='background:#eee; border:1px solid #b8b8b8; border-radius:5px; box-shadow: 0px 0px 8px rgba(0%,0%,0%,0.25); margin:0; padding:3px 0; position:fixed; visibility:hidden;'></ul>\"\n",
       "        var menu = wrapper.firstChild;\n",
       "\n",
       "        root.appendChild(menu);\n",
       "\n",
       "        var items = [];\n",
       "\n",
       "        var ignore_mouseup = null;\n",
       "        function open_menu(e)\n",
       "        {\n",
       "            var show_menu = false;\n",
       "            for(var index=0; index != items.length; ++index)\n",
       "            {\n",
       "                var item = items[index];\n",
       "                if(item.show(e))\n",
       "                {\n",
       "                    item.item.style.display = \"block\";\n",
       "                    show_menu = true;\n",
       "                }\n",
       "                else\n",
       "                {\n",
       "                    item.item.style.display = \"none\";\n",
       "                }\n",
       "            }\n",
       "\n",
       "            if(show_menu)\n",
       "            {\n",
       "                ignore_mouseup = true;\n",
       "                menu.style.left = (e.clientX + 1) + \"px\";\n",
       "                menu.style.top = (e.clientY - 5) + \"px\";\n",
       "                menu.style.visibility = \"visible\";\n",
       "                e.stopPropagation();\n",
       "                e.preventDefault();\n",
       "            }\n",
       "        }\n",
       "\n",
       "        function close_menu()\n",
       "        {\n",
       "            menu.style.visibility = \"hidden\";\n",
       "        }\n",
       "\n",
       "        function contextmenu(e)\n",
       "        {\n",
       "            open_menu(e);\n",
       "        }\n",
       "\n",
       "        function mousemove(e)\n",
       "        {\n",
       "            ignore_mouseup = false;\n",
       "        }\n",
       "\n",
       "        function mouseup(e)\n",
       "        {\n",
       "            if(ignore_mouseup)\n",
       "            {\n",
       "                ignore_mouseup = false;\n",
       "                return;\n",
       "            }\n",
       "            close_menu();\n",
       "        }\n",
       "\n",
       "        function keydown(e)\n",
       "        {\n",
       "            if(e.key == \"Escape\" || e.key == \"Esc\" || e.keyCode == 27)\n",
       "            {\n",
       "                close_menu();\n",
       "            }\n",
       "        }\n",
       "\n",
       "        canvas.addEventListener(\"contextmenu\", contextmenu);\n",
       "        canvas.addEventListener(\"mousemove\", mousemove);\n",
       "        document.addEventListener(\"mouseup\", mouseup);\n",
       "        document.addEventListener(\"keydown\", keydown);\n",
       "\n",
       "        var module = {};\n",
       "        module.add_item = function(label, show_callback, choose_callback)\n",
       "        {\n",
       "            var wrapper = document.createElement(\"div\");\n",
       "            wrapper.innerHTML = \"<li class='toyplot-context-menu-item' style='background:#eee; color:#333; padding:2px 20px; list-style:none; margin:0; text-align:left;'>\" + label + \"</li>\"\n",
       "            var item = wrapper.firstChild;\n",
       "\n",
       "            items.push({item: item, show: show_callback});\n",
       "\n",
       "            function mouseover()\n",
       "            {\n",
       "                this.style.background = \"steelblue\";\n",
       "                this.style.color = \"white\";\n",
       "            }\n",
       "\n",
       "            function mouseout()\n",
       "            {\n",
       "                this.style.background = \"#eee\";\n",
       "                this.style.color = \"#333\";\n",
       "            }\n",
       "\n",
       "            function choose_item(e)\n",
       "            {\n",
       "                close_menu();\n",
       "                choose_callback();\n",
       "\n",
       "                e.stopPropagation();\n",
       "                e.preventDefault();\n",
       "            }\n",
       "\n",
       "            item.addEventListener(\"mouseover\", mouseover);\n",
       "            item.addEventListener(\"mouseout\", mouseout);\n",
       "            item.addEventListener(\"mouseup\", choose_item);\n",
       "            item.addEventListener(\"contextmenu\", choose_item);\n",
       "\n",
       "            menu.appendChild(item);\n",
       "        };\n",
       "        return module;\n",
       "    })(modules[\"toyplot/root\"],modules[\"toyplot/canvas\"]);\n",
       "modules[\"toyplot/io\"] = (function()\n",
       "    {\n",
       "        var module = {};\n",
       "        module.save_file = function(mime_type, charset, data, filename)\n",
       "        {\n",
       "            var uri = \"data:\" + mime_type + \";charset=\" + charset + \",\" + data;\n",
       "            uri = encodeURI(uri);\n",
       "\n",
       "            var link = document.createElement(\"a\");\n",
       "            if(typeof link.download != \"undefined\")\n",
       "            {\n",
       "              link.href = uri;\n",
       "              link.style = \"visibility:hidden\";\n",
       "              link.download = filename;\n",
       "\n",
       "              document.body.appendChild(link);\n",
       "              link.click();\n",
       "              document.body.removeChild(link);\n",
       "            }\n",
       "            else\n",
       "            {\n",
       "              window.open(uri);\n",
       "            }\n",
       "        };\n",
       "        return module;\n",
       "    })();\n",
       "(function(tables, context_menu, io, owner_id, key, label, names, columns, filename)\n",
       "        {\n",
       "            tables.store(owner_id, key, names, columns);\n",
       "\n",
       "            var owner = document.querySelector(\"#\" + owner_id);\n",
       "            function show_item(e)\n",
       "            {\n",
       "                return owner.contains(e.target);\n",
       "            }\n",
       "\n",
       "            function choose_item()\n",
       "            {\n",
       "                io.save_file(\"text/csv\", \"utf-8\", tables.get_csv(owner_id, key), filename + \".csv\");\n",
       "            }\n",
       "\n",
       "            context_menu.add_item(\"Save \" + label + \" as CSV\", show_item, choose_item);\n",
       "        })(modules[\"toyplot/tables\"],modules[\"toyplot/menus/context\"],modules[\"toyplot/io\"],\"t61b531b21e3b4dbfa81c115ea7e1ee7b\",\"vertex_data\",\"graph vertex data\",[\"x\", \"y\"],[[-6.0, -6.0, -1.0, -6.0, -2.0, -6.0, -5.0, -1.0, -1.0, 0.0, -1.0, 0.0, -2.0, -2.0, -1.0, -2.0, -1.0, -5.0, -5.0, 0.0, -5.0, -4.0, -1.0, -1.0, 0.0, -1.0, 0.0, -1.0, -1.0, 0.0, -1.0, 0.0, -4.0, -4.0, 0.0, -4.0, -3.0, -3.0, -3.0, 0.0, -3.0, -2.0, -2.0, -2.0, -1.0, -2.0, -1.0, -1.0, -1.0, 0.0, -1.0, 0.0, -1.0, -1.0, 0.0, -1.0, 0.0], [8.3125, 11.5, 11.5, 8.5, 8.5, 4.9375, 4.9375, 11.5, 12.0, 12.0, 11.0, 11.0, 8.5, 9.5, 9.5, 7.5, 7.5, 4.9375, 6.0, 6.0, 3.875, 3.875, 9.5, 10.0, 10.0, 9.0, 9.0, 7.5, 8.0, 8.0, 7.0, 7.0, 3.875, 5.0, 5.0, 2.75, 2.75, 2.75, 4.0, 4.0, 1.5, 1.5, 1.5, 2.5, 2.5, 0.5, 0.5, 2.5, 3.0, 3.0, 2.0, 2.0, 0.5, 1.0, 1.0, 0.0, 0.0]],\"toyplot\");\n",
       "(function(tables, context_menu, io, owner_id, key, label, names, columns, filename)\n",
       "        {\n",
       "            tables.store(owner_id, key, names, columns);\n",
       "\n",
       "            var owner = document.querySelector(\"#\" + owner_id);\n",
       "            function show_item(e)\n",
       "            {\n",
       "                return owner.contains(e.target);\n",
       "            }\n",
       "\n",
       "            function choose_item()\n",
       "            {\n",
       "                io.save_file(\"text/csv\", \"utf-8\", tables.get_csv(owner_id, key), filename + \".csv\");\n",
       "            }\n",
       "\n",
       "            context_menu.add_item(\"Save \" + label + \" as CSV\", show_item, choose_item);\n",
       "        })(modules[\"toyplot/tables\"],modules[\"toyplot/menus/context\"],modules[\"toyplot/io\"],\"t61b531b21e3b4dbfa81c115ea7e1ee7b\",\"edge_data\",\"graph edge data\",[\"source\", \"target\"],[[0, 1, 0, 3, 0, 5, 7, 8, 7, 10, 12, 13, 12, 15, 17, 18, 17, 20, 22, 23, 22, 25, 27, 28, 27, 30, 32, 33, 32, 35, 37, 38, 37, 40, 42, 43, 42, 45, 47, 48, 47, 50, 52, 53, 52, 55], [1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 13, 14, 15, 16, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 38, 39, 40, 41, 43, 44, 45, 46, 48, 49, 50, 51, 53, 54, 55, 56]],\"toyplot\");\n",
       "(function(tables, context_menu, io, owner_id, key, label, names, columns, filename)\n",
       "        {\n",
       "            tables.store(owner_id, key, names, columns);\n",
       "\n",
       "            var owner = document.querySelector(\"#\" + owner_id);\n",
       "            function show_item(e)\n",
       "            {\n",
       "                return owner.contains(e.target);\n",
       "            }\n",
       "\n",
       "            function choose_item()\n",
       "            {\n",
       "                io.save_file(\"text/csv\", \"utf-8\", tables.get_csv(owner_id, key), filename + \".csv\");\n",
       "            }\n",
       "\n",
       "            context_menu.add_item(\"Save \" + label + \" as CSV\", show_item, choose_item);\n",
       "        })(modules[\"toyplot/tables\"],modules[\"toyplot/menus/context\"],modules[\"toyplot/io\"],\"t4f0ba7ba20e34ddb9bba73750915d55b\",\"data\",\"scatterplot\",[\"x\", \"y0\"],[[-6.0, -1.0, -2.0, -1.0, -1.0, -5.0, -4.0, -3.0, -2.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [8.3125, 11.5, 8.5, 9.5, 7.5, 4.9375, 3.875, 2.75, 1.5, 2.5, 0.5, 12.0, 11.0, 10.0, 9.0, 8.0, 7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0]],\"toyplot\");\n",
       "})();</script></div></div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## plot the resulting unrooted tree\n",
    "import toytree\n",
    "tre = toytree.tree(tet.trees.nhx)\n",
    "tre.draw(\n",
    "    width=350, \n",
    "    node_labels=tre.get_node_values(\"support\"),\n",
    "    );"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "## save the tree as a pdf\n",
    "import toyplot.pdf\n",
    "toyplot.pdf.render(canvas, \"analysis-tetrad/tetrad-tree.pdf\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### What does *tetrad* do differently from *svdquartets*?\n",
    "\n",
    "Not too much currently. But we have plans to expand it. Importantly, however, the code is open source meaning that anybody can read it and contribute it, which is not the case for Paup\\*. *tetrad* is also easier to install using conda and therefore easier to setup on an HPC cluster or local machine, and it can be parallelized across an arbitrarily large number of compute nodes while retaining a super small memory footprint."
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}