{"cells": [{"cell_type": "markdown", "metadata": {}, "source": ["# ete3\n", "\n", "[ete3](http://etetoolkit.org/) draws nice trees."]}, {"cell_type": "markdown", "metadata": {}, "source": ["[documentation](http://etetoolkit.org/docs/latest/index.html) [source](https://github.com/etetoolkit/ete/tree/master/ete3) [installation](https://pypi.python.org/pypi/ete3/) [tutorial](http://etetoolkit.org/docs/latest/tutorial/index.html) [gallery](http://etetoolkit.org/gallery/) [notebook](https://www.mrnoutahi.com/2016/01/09/Tree-manipulation-with-ETE/)"]}, {"cell_type": "code", "execution_count": 1, "metadata": {"collapsed": false}, "outputs": [{"data": {"text/html": ["<div id=\"my_id_menu_nb\">run previous cell, wait for 2 seconds</div>\n", "<script>\n", "function repeat_indent_string(n){\n", "    var a = \"\" ;\n", "    for ( ; n > 0 ; --n) {\n", "        a += \"    \";\n", "    }\n", "    return a;\n", "}\n", "var update_menu_string = function(begin, lfirst, llast, sformat, send, keep_item) {\n", "    var anchors = document.getElementsByClassName(\"section\");\n", "    if (anchors.length == 0) {\n", "        anchors = document.getElementsByClassName(\"text_cell_render rendered_html\");\n", "    }\n", "    var i,t;\n", "    var text_menu = begin;\n", "    var text_memo = \"<pre>\\nlength:\" + anchors.length + \"\\n\";\n", "    var ind = \"\";\n", "    var memo_level = 1;\n", "    var href;\n", "    var tags = [];\n", "    var main_item = 0;\n", "    for (i = 0; i <= llast; i++) {\n", "        tags.push(\"h\" + i);\n", "    }\n", "\n", "    for (i = 0; i < anchors.length; i++) {\n", "        text_memo += \"**\" + anchors[i].id + \"--\\n\";\n", "\n", "        var child = null;\n", "        for(t = 0; t < tags.length; t++) {\n", "            var r = anchors[i].getElementsByTagName(tags[t]);\n", "            if (r.length > 0) {\n", "child = r[0];\n", "break;\n", "            }\n", "        }\n", "        if (child == null){\n", "            text_memo += \"null\\n\";\n", "            continue;\n", "        }\n", "        if (anchors[i].hasAttribute(\"id\")) {\n", "            // when converted in RST\n", "            href = anchors[i].id;\n", "            text_memo += \"#1-\" + href;\n", "            // passer \u00e0 child suivant (le chercher)\n", "        }\n", "        else if (child.hasAttribute(\"id\")) {\n", "            // in a notebook\n", "            href = child.id;\n", "            text_memo += \"#2-\" + href;\n", "        }\n", "        else {\n", "            text_memo += \"#3-\" + \"*\" + \"\\n\";\n", "            continue;\n", "        }\n", "        var title = child.textContent;\n", "        var level = parseInt(child.tagName.substring(1,2));\n", "\n", "        text_memo += \"--\" + level + \"?\" + lfirst + \"--\" + title + \"\\n\";\n", "\n", "        if ((level < lfirst) || (level > llast)) {\n", "            continue ;\n", "        }\n", "        if (title.endsWith('\u00b6')) {\n", "            title = title.substring(0,title.length-1).replace(\"<\", \"&lt;\").replace(\">\", \"&gt;\").replace(\"&\", \"&amp;\")\n", "        }\n", "\n", "        if (title.length == 0) {\n", "            continue;\n", "        }\n", "\n", "        while (level < memo_level) {\n", "            text_menu += \"</ul>\\n\";\n", "            memo_level -= 1;\n", "        }\n", "        if (level == lfirst) {\n", "            main_item += 1;\n", "        }\n", "        if (keep_item != -1 && main_item != keep_item + 1) {\n", "            // alert(main_item + \" - \" + level + \" - \" + keep_item);\n", "            continue;\n", "        }\n", "        while (level > memo_level) {\n", "            text_menu += \"<ul>\\n\";\n", "            memo_level += 1;\n", "        }\n", "        text_menu += repeat_indent_string(level-2) + sformat.replace(\"__HREF__\", href).replace(\"__TITLE__\", title);\n", "    }\n", "    while (1 < memo_level) {\n", "        text_menu += \"</ul>\\n\";\n", "        memo_level -= 1;\n", "    }\n", "    text_menu += send;\n", "    //text_menu += \"\\n\" + text_memo;\n", "    return text_menu;\n", "};\n", "var update_menu = function() {\n", "    var sbegin = \"\";\n", "    var sformat = '<li><a href=\"#__HREF__\">__TITLE__</a></li>';\n", "    var send = \"\";\n", "    var keep_item = -1;\n", "    var text_menu = update_menu_string(sbegin, 2, 4, sformat, send, keep_item);\n", "    var menu = document.getElementById(\"my_id_menu_nb\");\n", "    menu.innerHTML=text_menu;\n", "};\n", "window.setTimeout(update_menu,2000);\n", "            </script>"], "text/plain": ["<IPython.core.display.HTML object>"]}, "execution_count": 2, "metadata": {}, "output_type": "execute_result"}], "source": ["from jyquickhelper import add_notebook_menu\n", "add_notebook_menu()"]}, {"cell_type": "markdown", "metadata": {}, "source": ["## example"]}, {"cell_type": "code", "execution_count": 2, "metadata": {"collapsed": false}, "outputs": [{"name": "stdout", "output_type": "stream", "text": ["Example numerical matrix\n", "\n", "#Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7\n", "A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58\n", "B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12\n", "C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36\n", "D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93\n", "E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65\n", "F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48\n", "G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26\n", "H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77\n", "\n"]}], "source": ["from ete3 import ClusterTree\n", "# Example of a minimalistic numerical matrix. It is encoded as a text\n", "# string for convenience, but it usally be loaded from a text file.\n", "matrix = \"\"\"\n", "#Names\\tcol1\\tcol2\\tcol3\\tcol4\\tcol5\\tcol6\\tcol7\n", "A\\t-1.23\\t-0.81\\t1.79\\t0.78\\t-0.42\\t-0.69\\t0.58\n", "B\\t-1.76\\t-0.94\\t1.16\\t0.36\\t0.41\\t-0.35\\t1.12\n", "C\\t-2.19\\t0.13\\t0.65\\t-0.51\\t0.52\\t1.04\\t0.36\n", "D\\t-1.22\\t-0.98\\t0.79\\t-0.76\\t-0.29\\t1.54\\t0.93\n", "E\\t-1.47\\t-0.83\\t0.85\\t0.07\\t-0.81\\t1.53\\t0.65\n", "F\\t-1.04\\t-1.11\\t0.87\\t-0.14\\t-0.80\\t1.74\\t0.48\n", "G\\t-1.57\\t-1.17\\t1.29\\t0.23\\t-0.20\\t1.17\\t0.26\n", "H\\t-1.53\\t-1.25\\t0.59\\t-0.30\\t0.32\\t1.41\\t0.77\n", "\"\"\"\n", "print(\"Example numerical matrix\")\n", "print(matrix)"]}, {"cell_type": "code", "execution_count": 3, "metadata": {"collapsed": false}, "outputs": [{"name": "stdout", "output_type": "stream", "text": ["\n", "         /-A\n", "      /-|\n", "     |   \\-B\n", "   /-|\n", "  |  |   /-C\n", "  |   \\-|\n", "  |     |   /-D\n", "--|      \\-|\n", "  |         \\-E\n", "  |\n", "  |   /-F\n", "   \\-|\n", "     |   /-G\n", "      \\-|\n", "         \\-H\n"]}], "source": ["t = ClusterTree(\"(((A,B),(C,(D,E))),(F,(G,H)));\", text_array=matrix)\n", "print(t)"]}, {"cell_type": "code", "execution_count": 4, "metadata": {"collapsed": false}, "outputs": [{"data": {"image/png": 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"text/plain": ["<IPython.core.display.Image object>"]}, "execution_count": 5, "metadata": {}, "output_type": "execute_result"}], "source": ["t.render(\"%%inline\", h=300)"]}, {"cell_type": "code", "execution_count": 5, "metadata": {"collapsed": true}, "outputs": [], "source": ["from ete3 import TreeStyle\n", "ts = TreeStyle()\n", "ts.show_branch_length = True # show branch length\n", "ts.show_branch_support = True # show support\n", "ts.show_leaf_name = True"]}, {"cell_type": "code", "execution_count": 6, "metadata": {"collapsed": false}, "outputs": [{"data": {"image/png": 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"text/plain": ["<IPython.core.display.Image object>"]}, "execution_count": 7, "metadata": {}, "output_type": "execute_result"}], "source": ["t.render(\"%%inline\",tree_style=ts)"]}, {"cell_type": "code", "execution_count": 7, "metadata": {"collapsed": false}, "outputs": [{"data": {"image/png": 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"text/plain": ["<IPython.core.display.Image object>"]}, "execution_count": 8, "metadata": {}, "output_type": "execute_result"}], "source": ["ts.layout_fn = \"heatmap\"\n", "t.render(\"%%inline\",tree_style=ts)"]}, {"cell_type": "code", "execution_count": 8, "metadata": {"collapsed": false}, "outputs": [{"data": {"image/png": 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UQdXmtbg9smUj03Z466W7zlLd9+13nv08IO39VD+f8o+3JC41ce6cdOOGZIz0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\n8alPRVPnb/82mjr76DWLQ+d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"text/plain": ["<IPython.core.display.Image object>"]}, "execution_count": 9, "metadata": {}, "output_type": "execute_result"}], "source": ["ts.layout_fn = \"cluster_cbars\"\n", "t.render(\"%%inline\",tree_style=ts)"]}, {"cell_type": "code", "execution_count": 9, "metadata": {"collapsed": false}, "outputs": [{"data": {"image/png": 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"text/plain": ["<IPython.core.display.Image object>"]}, "execution_count": 10, "metadata": {}, "output_type": "execute_result"}], "source": ["ts.layout_fn = \"cluster_bars\"\n", "t.render(\"%%inline\",tree_style=ts)"]}, {"cell_type": "code", "execution_count": 10, "metadata": {"collapsed": false}, "outputs": [{"data": {"image/png": 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2M9y8eROPHj0aLmdwyiAOjMimS5eAK1esJLybm2kfzbikshvMWtasASqt0Xpx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\nTq9X0VP7aNsLCg3sqQqKY9G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"text/plain": ["<IPython.core.display.Image object>"]}, "execution_count": 11, "metadata": {}, "output_type": "execute_result"}], "source": ["ts.layout_fn = \"cluster_lines\"\n", "t.render(\"%%inline\",tree_style=ts)"]}, {"cell_type": "code", "execution_count": 11, "metadata": {"collapsed": true}, "outputs": [], "source": []}], "metadata": {"kernelspec": {"display_name": "Python 3", "language": "python", "name": "python3"}, "language_info": {"codemirror_mode": {"name": "ipython", "version": 3}, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.5.2"}}, "nbformat": 4, "nbformat_minor": 2}