Muscari_CP_TreePlotting.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "34cae815-90b8-4dac-8287-f8a9cb51e3b7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ipyrad v. 0.9.71\n",
      "toytree v. 2.0.5\n",
      "Python v. 3.9.2\n"
     ]
    }
   ],
   "source": [
    "## import\n",
    "import ipyrad as ip\n",
    "import ipyrad.analysis as ipa\n",
    "import ipyparallel as ipp\n",
    "import pandas as pd\n",
    "import toytree\n",
    "import toyplot\n",
    "\n",
    "## print Version of ipyrad und toytree\n",
    "print(\"ipyrad v. {}\".format(ip.__version__))\n",
    "print(\"toytree v. {}\".format(toytree.__version__))\n",
    "\n",
    "## print Version of Python\n",
    "from platform import python_version\n",
    "print(\"Python v.\", python_version())"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a926cc03",
   "metadata": {},
   "source": [
    "## Plotting MrBayes Tree without indel codding"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "a6e13f0f-65ae-4898-9851-efa83a1cee4f",
   "metadata": {},
   "outputs": [
    {
     "data": {
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     "metadata": {},
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   ],
   "source": [
    "## assign tree and location to variable\n",
    "mbtree = \"/home/tim/Phylo/Muscari_CP/Mus_CP_MrBayes_20210811/Muscari_CP_HSEX_INVREF_MrBayes_cons.tre\"\n",
    "\n",
    "## load from the .trees attribute or from the saved tree file\n",
    "tre = toytree.tree(mbtree, tree_format=10).root(wildcard = \"Brimeura\")\n",
    "\n",
    "## draw the tree with styling\n",
    "canvas, axes, mark = tre.ladderize(1).draw(\n",
    "    width = 900,\n",
    "    height = 900,\n",
    "    tip_labels_align=True,\n",
    "    scalebar=True,\n",
    "    tip_labels_style = {\"font-size\": \"11px\"},\n",
    "    node_labels='prob',\n",
    "    node_sizes=0,\n",
    "    node_labels_style={\"font-size\": \"12px\",\n",
    "                       \"baseline-shift\": \"7px\",\n",
    "                       \"-toyplot-anchor-shift\": \"-13px\"},\n",
    ");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "b87f4ccc",
   "metadata": {},
   "outputs": [],
   "source": [
    "import toyplot.pdf\n",
    "toyplot.pdf.render(canvas, \"/home/tim/Phylo/Muscari_CP/Mus_CP_MrBayes_20210811/Muscari_CP_MrBayes_20210811.pdf\");"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "db9611dc",
   "metadata": {},
   "source": [
    "## Plotting MrBayes Tree with simple indel codding (SIC)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "4ac9fd1b-7697-4ffa-b31d-94f63678f3c4",
   "metadata": {},
   "outputs": [
    {
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## assign tree and location to variable\n",
    "mbsictree = \"/home/tim/Phylo/Muscari_CP/Mus_CP_MrBayes_SIC_20210811/Muscari_CP_HSEX_INVREF_SIC_MrBayes_con.tre\"\n",
    "\n",
    "## load from the .trees attribute or from the saved tree file\n",
    "tre = toytree.tree(mbsictree, tree_format=10).root(wildcard = \"Brimeura\")\n",
    "\n",
    "## draw the tree with styling\n",
    "canvas, axes, mark = tre.ladderize(1).draw(\n",
    "    width = 900,\n",
    "    height = 900,\n",
    "    tip_labels_align=True,\n",
    "    scalebar=True,\n",
    "    tip_labels_style = {\"font-size\": \"11px\"},\n",
    "    node_labels='prob',\n",
    "    node_sizes=0,\n",
    "    node_labels_style={\"font-size\": \"12px\",\n",
    "                       \"baseline-shift\": \"7px\",\n",
    "                       \"-toyplot-anchor-shift\": \"-13px\"},\n",
    ");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "cd83f3f1",
   "metadata": {},
   "outputs": [],
   "source": [
    "import toyplot.pdf\n",
    "toyplot.pdf.render(canvas, \"/home/tim/Phylo/Muscari_CP/Mus_CP_MrBayes_SIC_20210811/Muscari_CP_MrBayes_SIC_20210811.pdf\");"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "54ad26e6",
   "metadata": {},
   "source": [
    "## Plotting RAxML Trees"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "6fc83365-f6a6-4752-95e1-2db7b4a31bc5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "unrecognized arguments skipped: ['use_edge_length']\n",
      "check the docs, argument names may have changed.\n"
     ]
    },
    {
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x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED3539</text></g><g transform=\"translate(644.45,105.30)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED3965</text></g><g transform=\"translate(644.45,90.94)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED1274</text></g><g transform=\"translate(644.45,76.58)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_weissii_W6081</text></g><g transform=\"translate(644.45,62.22)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED1256</text></g></g></g></g></g></svg><div class=\"toyplot-behavior\"><script>(function()\n",
       "{\n",
       "var modules={};\n",
       "})();</script></div></div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "Mus_CP_ML = toytree.tree(\"/home/tim/Phylo/Muscari_CP/Mus_CP_RAxML_20210811/Mus_CP_RAxML_20210811.tre\")\n",
    "\n",
    "rtre = Mus_CP_ML.root(wildcard = \"Brim\")\n",
    "\n",
    "# use canvas and axes function in order use export function\n",
    "canvas, axes, mark = rtre.ladderize(1).draw(\n",
    "    width = 900,\n",
    "    height = 900,\n",
    "    tip_labels_align = True,\n",
    "    tip_labels_style = {\"font-size\": \"11px\"},\n",
    "    node_labels='support',\n",
    "    node_sizes=0,\n",
    "    node_labels_style={\"font-size\": \"12px\",\n",
    "                       \"baseline-shift\": \"7px\",\n",
    "                       \"-toyplot-anchor-shift\": \"-13px\"},\n",
    "    );"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "3cecee92",
   "metadata": {},
   "outputs": [],
   "source": [
    "import toyplot.pdf\n",
    "toyplot.pdf.render(canvas, \"/home/tim/Phylo/Muscari_CP/Mus_CP_RAxML_20210811/Mus_CP_RAxML_20210811.pdf\");"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1605c04a",
   "metadata": {},
   "source": [
    "## Plotting IQtree Trees"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "a7eb608c",
   "metadata": {},
   "outputs": [
    {
     "data": {
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transform=\"translate(644.45,450.00)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_anatolicum_W6087</text></g><g transform=\"translate(644.45,435.64)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_sivrihisardaghlarensis_ED1278</text></g><g transform=\"translate(644.45,421.28)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Pseudomuscari_coeruleum_ED1261</text></g><g transform=\"translate(644.45,406.91)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Pseudomuscari_pallens_ED1267</text></g><g transform=\"translate(644.45,392.55)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_aucheri</text></g><g transform=\"translate(644.45,378.19)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_armeniacum_ED1244</text></g><g transform=\"translate(644.45,363.83)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_armeniacum_W6089</text></g><g transform=\"translate(644.45,349.46)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_neumannii_ED1607</text></g><g transform=\"translate(644.45,335.10)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_neumannii_HT_ED1243</text></g><g transform=\"translate(644.45,320.74)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_kerkis_ED1280</text></g><g transform=\"translate(644.45,306.38)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_pulchellum_ED3231</text></g><g transform=\"translate(644.45,292.01)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_microstomum</text></g><g transform=\"translate(644.45,277.65)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_latifolium_ED1265</text></g><g transform=\"translate(644.45,263.29)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_bourgaei_ED1259</text></g><g transform=\"translate(644.45,248.93)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_turcicum</text></g><g transform=\"translate(644.45,234.56)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_longipes_ED3233</text></g><g transform=\"translate(644.45,220.20)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_babachii</text></g><g transform=\"translate(644.45,205.84)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Muscari_erdalii</text></g><g transform=\"translate(644.45,191.48)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_spreitzenhoferii_ED1248</text></g><g transform=\"translate(644.45,177.11)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopolida_cycladica_W6082</text></g><g transform=\"translate(644.45,162.75)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_tenuiflora_ED1263</text></g><g transform=\"translate(644.45,148.39)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_caucasica_ED1262</text></g><g transform=\"translate(644.45,134.03)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_matritensis_ED1282</text></g><g transform=\"translate(644.45,119.66)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED3539</text></g><g transform=\"translate(644.45,105.30)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED3965</text></g><g transform=\"translate(644.45,90.94)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED1274</text></g><g transform=\"translate(644.45,76.58)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_comosa_ED1256</text></g><g transform=\"translate(644.45,62.22)rotate(0)\"><text x=\"15.00\" y=\"2.81\" style=\"\">Leopoldia_weissii_W6081</text></g></g></g></g></g></svg><div class=\"toyplot-behavior\"><script>(function()\n",
       "{\n",
       "var modules={};\n",
       "})();</script></div></div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "Mus_CP_ML = toytree.tree(\"/home/tim/Phylo/Muscari_CP/Mus_CP_IQtree_20210811/Mus_CP_IQtree_20210811.tre\")\n",
    "\n",
    "rtre = Mus_CP_ML.root(wildcard = \"Brim\")\n",
    "\n",
    "# use canvas and axes function in order use export function\n",
    "canvas, axes, mark = rtre.ladderize(1).draw(\n",
    "    width = 900,\n",
    "    height = 900,\n",
    "    tip_labels_align = True,\n",
    "    tip_labels_style = {\"font-size\": \"11px\"},\n",
    "    node_labels='support',\n",
    "    node_sizes=0,\n",
    "    node_labels_style={\"font-size\": \"12px\",\n",
    "                       \"baseline-shift\": \"7px\",\n",
    "                       \"-toyplot-anchor-shift\": \"-13px\"},\n",
    "    );"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "9a7c8d3a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import toyplot.pdf\n",
    "toyplot.pdf.render(canvas, \"/home/tim/Phylo/Muscari_CP/Mus_CP_IQtree_20210811/Mus_CP_IQtree_20210811.pdf\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "id": "b4e48f87-08e7-489b-8a76-cc5f22c3d158",
   "metadata": {},
   "outputs": [],
   "source": [
    "## Plotting ML and Bayes Tree beside each other"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "706b020f-4891-4436-ada0-749aef542889",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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