{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
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   "source": [
    "# Display a Phylogenetic Tree with a Circular Dendrogram Style"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
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\"zerolinecolor\": \"white\", \"zerolinewidth\": 2}}}, \"width\": 600, \"xaxis\": {\"range\": [-0.4049606955627233, 0.7256381452272351], \"visible\": false}, \"yaxis\": {\"range\": [-0.5676579357018365, 0.562940905088122], \"visible\": false}},\n",
       "                        {\"responsive\": true}\n",
       "                    ).then(function(){\n",
       "                            \n",
       "var gd = document.getElementById('efac30f1-6600-48e0-8418-e04b69cba934');\n",
       "var x = new MutationObserver(function (mutations, observer) {{\n",
       "        var display = window.getComputedStyle(gd).display;\n",
       "        if (!display || display === 'none') {{\n",
       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
       "        }}\n",
       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
       "}}\n",
       "\n",
       "// Listen for the clearing of the current output cell\n",
       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
       "}}\n",
       "\n",
       "                        })\n",
       "                };\n",
       "                });\n",
       "            </script>\n",
       "        </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from cogent3.app import io\n",
    "\n",
    "reader = io.load_json()\n",
    "\n",
    "ens_tree = reader(\"../data/GN-tree.json\")\n",
    "fig = ens_tree.get_figure(\"circular\", width=600, height=600)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Colouring a set of edges"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "                'plotly': ['https://cdn.plot.ly/plotly-latest.min']\n",
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       "        require(['plotly'], function(Plotly) {\n",
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       "        </script>\n",
       "        "
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       "var x = new MutationObserver(function (mutations, observer) {{\n",
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       "        if (!display || display === 'none') {{\n",
       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
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       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
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       "\n",
       "// Listen for the clearing of the current output cell\n",
       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
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       "\n",
       "                        })\n",
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       "                });\n",
       "            </script>\n",
       "        </div>"
      ]
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   ],
   "source": [
    "fig.style_edges(\"AfricanEl\", tip2=\"Manatee\", legendgroup=\"Afrotheria\",\n",
    "                line=dict(color=\"magenta\"))\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## With Contemporaneous Tips"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
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