salmonid species tree.ipynb

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   "cell_type": "code",
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   "source": [
    "import ete2"
   ]
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   "cell_type": "code",
   "execution_count": 13,
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    "collapsed": false
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   "source": [
    "from ete2 import Tree\n",
    "t = Tree() # Creates an empty tree\n",
    "\n",
    "esox1 = t.add_child(name=\"Esox\\n(pike)\", dist = 4) # Adds a second child to the current tree\n",
    "                           # root and returns it\n",
    "#esox2 = esox1.add_child(name=\"Esox\\n(pike)\", dist = 1) # Adds a second child to the current tree\n",
    "    \n",
    "salmonid = t.add_child(name=\"salmonid\", dist = 1) # Adds a new child to the current tree root\n",
    "                           # and returns it\n",
    "    \n",
    "salmon = salmonid.add_child(name=\"salmon\", dist = 1.5) # Adds a new child to one of the branches\n",
    "rest = salmonid.add_child(name=\"rest\") # Adds a new child to one of the branches\n",
    "Thymallinae = rest.add_child(name=\"Thymallinae\\n(graylings)\") # Adds a new child to one of the branches\n",
    "Coregoninae = rest.add_child(name=\"Coregoninae\\n(whitefish & ciscoes)\") # Adds a new child to one of the branches\n",
    "Salmo = salmon.add_child(name=\"Salmo Salar\\n(Atlantic salmon)\") # Adds a new child to one of the branches\n",
    "Oncorhynchus = salmon.add_child(name=\"Oncorhynchus keta\\n (chum salmon)\") # Adds a new child to one of the branches\n",
    "\n",
    "#t.set_outgroup( t&\"Esox (pike)\" )\n",
    "\n",
    "# format style\n",
    "ts = ete2.TreeStyle()\n",
    "ts.show_leaf_name = True\n",
    "#ts.force_topology = True\n",
    "ts.optimal_scale_level = 'full'\n",
    "ts.branch_vertical_margin = 4\n",
    "ts.show_scale = False\n",
    "ts.scale = 25\n",
    "\n",
    "salmonid.img_style[\"size\"] = 30\n",
    "\n",
    "ns0 = ete2.NodeStyle()\n",
    "ns0[\"size\"] = 0\n",
    "\n",
    "\n",
    "ns1 = ete2.NodeStyle()\n",
    "ns1[\"size\"] = 20\n",
    "ns1[\"vt_line_color\"] = \"#fd3c06\"\n",
    "#ns1[\"hz_line_color\"] = \"#ff0000\"\n",
    "ns1[\"vt_line_width\"] = 2\n",
    "#ns1[\"hz_line_width\"] = 2\n",
    "ns1[\"fgcolor\"] = '#fd3c06'\n",
    "\n",
    "ns2 = ete2.NodeStyle()\n",
    "ns2[\"size\"] = 0\n",
    "ns2[\"vt_line_color\"] = \"#fd3c06\"\n",
    "ns2[\"hz_line_color\"] = \"#fd3c06\"\n",
    "ns2[\"hz_line_width\"] = 2\n",
    "ns2[\"vt_line_width\"] = 2\n",
    "\n",
    "for n in t.traverse():\n",
    "    n.set_style(ns0)\n",
    "    \n",
    "salmonid.set_style(ns1)\n",
    "for l in salmonid.iter_leaves():\n",
    "        l.img_style = ns2\n",
    "salmonid.children[0].img_style = ns2\n",
    "salmonid.children[1].img_style = ns2\n",
    "   \n",
    "render = t.render('tree.png', tree_style=ts, units = 'px', h = 450)"
   ]
  },
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   "execution_count": null,
   "metadata": {
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