05_Graphic_in_Python.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#  Grpahic in Pyhton for Genomic data science"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "https://demo.bokeh.org/\n",
    "\n",
    "https://python.arviz.org/en/0.14.0/index.html\n",
    "\n",
    "https://github.com/spotify/chartify/blob/master/examples/Examples.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "#pip install bokeh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       "        .bk-notebook-logo {\n",
       "            display: block;\n",
       "            width: 20px;\n",
       "            height: 20px;\n",
       "            background-image: url(data:image/png;base64,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);\n",
       "        }\n",
       "    </style>\n",
       "    <div>\n",
       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-notebook-logo\"></a>\n",
       "        <span id=\"p1141\">Loading BokehJS ...</span>\n",
       "    </div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": "(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\nconst JS_MIME_TYPE = 'application/javascript';\n  const HTML_MIME_TYPE = 'text/html';\n  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n  const CLASS_NAME = 'output_bokeh rendered_html';\n\n  /**\n   * Render data to the DOM node\n   */\n  function render(props, node) {\n    const script = document.createElement(\"script\");\n    node.appendChild(script);\n  }\n\n  /**\n   * Handle when an output is cleared or removed\n   */\n  function handleClearOutput(event, handle) {\n    const cell = handle.cell;\n\n    const id = cell.output_area._bokeh_element_id;\n    const server_id = cell.output_area._bokeh_server_id;\n    // Clean up Bokeh references\n    if (id != null && id in Bokeh.index) {\n      Bokeh.index[id].model.document.clear();\n      delete Bokeh.index[id];\n    }\n\n    if (server_id !== undefined) {\n      // Clean up Bokeh references\n      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n      cell.notebook.kernel.execute(cmd_clean, {\n        iopub: {\n          output: function(msg) {\n            const id = msg.content.text.trim();\n            if (id in Bokeh.index) {\n              Bokeh.index[id].model.document.clear();\n              delete Bokeh.index[id];\n            }\n          }\n        }\n      });\n      // Destroy server and session\n      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n      cell.notebook.kernel.execute(cmd_destroy);\n    }\n  }\n\n  /**\n   * Handle when a new output is added\n   */\n  function handleAddOutput(event, handle) {\n    const output_area = handle.output_area;\n    const output = handle.output;\n\n    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n      return\n    }\n\n    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n\n    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n      // store reference to embed id on output_area\n      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n    }\n    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n      const bk_div = document.createElement(\"div\");\n      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n      const script_attrs = bk_div.children[0].attributes;\n      for (let i = 0; i < script_attrs.length; i++) {\n        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n      }\n      // store reference to server id on output_area\n      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n    }\n  }\n\n  function register_renderer(events, OutputArea) {\n\n    function append_mime(data, metadata, element) {\n      // create a DOM node to render to\n      const toinsert = this.create_output_subarea(\n        metadata,\n        CLASS_NAME,\n        EXEC_MIME_TYPE\n      );\n      this.keyboard_manager.register_events(toinsert);\n      // Render to node\n      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n      render(props, toinsert[toinsert.length - 1]);\n      element.append(toinsert);\n      return toinsert\n    }\n\n    /* Handle when an output is cleared or removed */\n    events.on('clear_output.CodeCell', handleClearOutput);\n    events.on('delete.Cell', handleClearOutput);\n\n    /* Handle when a new output is added */\n    events.on('output_added.OutputArea', handleAddOutput);\n\n    /**\n     * Register the mime type and append_mime function with output_area\n     */\n    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n      /* Is output safe? */\n      safe: true,\n      /* Index of renderer in `output_area.display_order` */\n      index: 0\n    });\n  }\n\n  // register the mime type if in Jupyter Notebook environment and previously unregistered\n  if (root.Jupyter !== undefined) {\n    const events = require('base/js/events');\n    const OutputArea = require('notebook/js/outputarea').OutputArea;\n\n    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n      register_renderer(events, OutputArea);\n    }\n  }\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(\"p1141\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.1.0.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n          for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\nif (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(\"p1141\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));",
      "application/vnd.bokehjs_load.v0+json": ""
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Grophic in Python # pip install bokeh\n",
    "from bokeh.io import output_notebook\n",
    "from bokeh.plotting import figure, show\n",
    "output_notebook()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "  <div id=\"40881986-3740-42a7-9a42-0958d34cf0a9\" data-root-id=\"p1142\" style=\"display: contents;\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": "(function(root) {\n  function embed_document(root) {\n  const docs_json = {\"a45bd93d-a716-456a-884d-2782c46273cf\":{\"version\":\"3.1.0\",\"title\":\"Bokeh Application\",\"defs\":[],\"roots\":[{\"type\":\"object\",\"name\":\"Figure\",\"id\":\"p1142\",\"attributes\":{\"width\":400,\"height\":400,\"x_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1144\"},\"y_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1143\"},\"x_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1155\"},\"y_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1157\"},\"title\":{\"type\":\"object\",\"name\":\"Title\",\"id\":\"p1148\"},\"renderers\":[{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1194\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1188\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1190\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1189\"},\"data\":{\"type\":\"map\",\"entries\":[[\"x\",[1,2,3,4,5]],[\"y\",[6,7,2,4,5]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1195\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1196\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1191\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":20},\"line_color\":{\"type\":\"value\",\"value\":\"navy\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.5},\"fill_color\":{\"type\":\"value\",\"value\":\"navy\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.5},\"hatch_color\":{\"type\":\"value\",\"value\":\"navy\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.5}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1192\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":20},\"line_color\":{\"type\":\"value\",\"value\":\"navy\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"navy\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_color\":{\"type\":\"value\",\"value\":\"navy\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1193\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":20},\"line_color\":{\"type\":\"value\",\"value\":\"navy\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"navy\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_color\":{\"type\":\"value\",\"value\":\"navy\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2}}}}}],\"toolbar\":{\"type\":\"object\",\"name\":\"Toolbar\",\"id\":\"p1146\",\"attributes\":{\"tools\":[{\"type\":\"object\",\"name\":\"PanTool\",\"id\":\"p1173\"},{\"type\":\"object\",\"name\":\"WheelZoomTool\",\"id\":\"p1174\"},{\"type\":\"object\",\"name\":\"BoxZoomTool\",\"id\":\"p1175\",\"attributes\":{\"overlay\":{\"type\":\"object\",\"name\":\"BoxAnnotation\",\"id\":\"p1176\",\"attributes\":{\"syncable\":false,\"level\":\"overlay\",\"visible\":false,\"left_units\":\"canvas\",\"right_units\":\"canvas\",\"bottom_units\":\"canvas\",\"top_units\":\"canvas\",\"line_color\":\"black\",\"line_alpha\":1.0,\"line_width\":2,\"line_dash\":[4,4],\"fill_color\":\"lightgrey\",\"fill_alpha\":0.5}}}},{\"type\":\"object\",\"name\":\"SaveTool\",\"id\":\"p1177\"},{\"type\":\"object\",\"name\":\"ResetTool\",\"id\":\"p1178\"},{\"type\":\"object\",\"name\":\"HelpTool\",\"id\":\"p1179\"}]}},\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1166\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1167\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1169\"},\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1168\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1159\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1160\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1162\"},\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1161\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1165\",\"attributes\":{\"axis\":{\"id\":\"p1159\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1172\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1166\"}}}]}}],\"callbacks\":{\"type\":\"map\"}}};\n  const render_items = [{\"docid\":\"a45bd93d-a716-456a-884d-2782c46273cf\",\"roots\":{\"p1142\":\"40881986-3740-42a7-9a42-0958d34cf0a9\"},\"root_ids\":[\"p1142\"]}];\n  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n  }\n  if (root.Bokeh !== undefined) {\n    embed_document(root);\n  } else {\n    let attempts = 0;\n    const timer = setInterval(function(root) {\n      if (root.Bokeh !== undefined) {\n        clearInterval(timer);\n        embed_document(root);\n      } else {\n        attempts++;\n        if (attempts > 100) {\n          clearInterval(timer);\n          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n        }\n      }\n    }, 10, root)\n  }\n})(window);",
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "p1142"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "p = figure(width=400, height=400)\n",
    "p.circle([1, 2, 3, 4, 5], [6, 7, 2, 4, 5], size=20, color=\"navy\", alpha=0.5)\n",
    "show(p)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "  <div id=\"1f1b904f-af76-4f9f-998f-d8423055e9c4\" data-root-id=\"p1295\" style=\"display: contents;\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": "(function(root) {\n  function embed_document(root) {\n  const docs_json = {\"4b61fab6-264a-4ed9-bf1e-8e8aa4867503\":{\"version\":\"3.1.0\",\"title\":\"Bokeh Application\",\"defs\":[],\"roots\":[{\"type\":\"object\",\"name\":\"Figure\",\"id\":\"p1295\",\"attributes\":{\"width\":500,\"height\":500,\"x_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1297\"},\"y_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1296\"},\"x_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1308\"},\"y_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1310\"},\"title\":{\"type\":\"object\",\"name\":\"Title\",\"id\":\"p1301\"},\"renderers\":[{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1347\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1341\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1343\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1342\"},\"data\":{\"type\":\"map\",\"entries\":[[\"x\",[1,3,2,2]],[\"y\",[1,2,1,2]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1348\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1349\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1344\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":{\"type\":\"value\",\"value\":\"blue\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.5},\"fill_color\":{\"type\":\"value\",\"value\":\"blue\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.5},\"hatch_color\":{\"type\":\"value\",\"value\":\"blue\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.5},\"radius\":{\"type\":\"value\",\"value\":0.35}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1345\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":{\"type\":\"value\",\"value\":\"blue\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"blue\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_color\":{\"type\":\"value\",\"value\":\"blue\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1},\"radius\":{\"type\":\"value\",\"value\":0.35}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1346\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":{\"type\":\"value\",\"value\":\"blue\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"blue\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_color\":{\"type\":\"value\",\"value\":\"blue\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2},\"radius\":{\"type\":\"value\",\"value\":0.35}}}}}],\"toolbar\":{\"type\":\"object\",\"name\":\"Toolbar\",\"id\":\"p1299\",\"attributes\":{\"tools\":[{\"type\":\"object\",\"name\":\"PanTool\",\"id\":\"p1326\"},{\"type\":\"object\",\"name\":\"WheelZoomTool\",\"id\":\"p1327\"},{\"type\":\"object\",\"name\":\"BoxZoomTool\",\"id\":\"p1328\",\"attributes\":{\"overlay\":{\"type\":\"object\",\"name\":\"BoxAnnotation\",\"id\":\"p1329\",\"attributes\":{\"syncable\":false,\"level\":\"overlay\",\"visible\":false,\"left_units\":\"canvas\",\"right_units\":\"canvas\",\"bottom_units\":\"canvas\",\"top_units\":\"canvas\",\"line_color\":\"black\",\"line_alpha\":1.0,\"line_width\":2,\"line_dash\":[4,4],\"fill_color\":\"lightgrey\",\"fill_alpha\":0.5}}}},{\"type\":\"object\",\"name\":\"SaveTool\",\"id\":\"p1330\"},{\"type\":\"object\",\"name\":\"ResetTool\",\"id\":\"p1331\"},{\"type\":\"object\",\"name\":\"HelpTool\",\"id\":\"p1332\"}]}},\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1319\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1320\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1322\"},\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1321\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1312\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1313\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1315\"},\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1314\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1318\",\"attributes\":{\"axis\":{\"id\":\"p1312\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1325\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1319\"}}}]}}],\"callbacks\":{\"type\":\"map\"}}};\n  const render_items = [{\"docid\":\"4b61fab6-264a-4ed9-bf1e-8e8aa4867503\",\"roots\":{\"p1295\":\"1f1b904f-af76-4f9f-998f-d8423055e9c4\"},\"root_ids\":[\"p1295\"]}];\n  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n  }\n  if (root.Bokeh !== undefined) {\n    embed_document(root);\n  } else {\n    let attempts = 0;\n    const timer = setInterval(function(root) {\n      if (root.Bokeh !== undefined) {\n        clearInterval(timer);\n        embed_document(root);\n      } else {\n        attempts++;\n        if (attempts > 100) {\n          clearInterval(timer);\n          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n        }\n      }\n    }, 10, root)\n  }\n})(window);",
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "p1295"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "#  Four circles with Bokeh # pip install bokeh\n",
    "\n",
    "from bokeh.plotting import figure, output_file, show\n",
    "p = figure(width=500, height=500)\n",
    "x = [1, 3, 2, 2]\n",
    "y = [1, 2, 1, 2]\n",
    "p.circle(x, y, radius=.35, alpha=0.5, color='blue') # radius: size of circle\n",
    "output_file('out.html')\n",
    "show(p)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "  <div id=\"393b272a-792a-4619-9dc5-a5769830dc0a\" data-root-id=\"p1547\" style=\"display: contents;\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": "(function(root) {\n  function embed_document(root) {\n  const docs_json = {\"cbc8ce46-4383-4c29-a889-5335e11ad457\":{\"version\":\"3.1.0\",\"title\":\"Bokeh Application\",\"defs\":[],\"roots\":[{\"type\":\"object\",\"name\":\"Figure\",\"id\":\"p1547\",\"attributes\":{\"x_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1549\"},\"y_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1548\"},\"x_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1561\"},\"y_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1563\"},\"title\":{\"type\":\"object\",\"name\":\"Title\",\"id\":\"p1550\",\"attributes\":{\"text\":\"Mean wt increased vs. time\"}},\"renderers\":[{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1600\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1594\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1596\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1595\"},\"data\":{\"type\":\"map\",\"entries\":[[\"x\",[1,2,3,4,5,6,7,8]],[\"y\",[0.7,1.4,2.1,3,3.85,4.55,5.8,6.45]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1601\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1602\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1597\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1598\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1599\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2}}}}}],\"toolbar\":{\"type\":\"object\",\"name\":\"Toolbar\",\"id\":\"p1553\",\"attributes\":{\"tools\":[{\"type\":\"object\",\"name\":\"PanTool\",\"id\":\"p1579\"},{\"type\":\"object\",\"name\":\"WheelZoomTool\",\"id\":\"p1580\"},{\"type\":\"object\",\"name\":\"BoxZoomTool\",\"id\":\"p1581\",\"attributes\":{\"overlay\":{\"type\":\"object\",\"name\":\"BoxAnnotation\",\"id\":\"p1582\",\"attributes\":{\"syncable\":false,\"level\":\"overlay\",\"visible\":false,\"left_units\":\"canvas\",\"right_units\":\"canvas\",\"bottom_units\":\"canvas\",\"top_units\":\"canvas\",\"line_color\":\"black\",\"line_alpha\":1.0,\"line_width\":2,\"line_dash\":[4,4],\"fill_color\":\"lightgrey\",\"fill_alpha\":0.5}}}},{\"type\":\"object\",\"name\":\"SaveTool\",\"id\":\"p1583\"},{\"type\":\"object\",\"name\":\"ResetTool\",\"id\":\"p1584\"},{\"type\":\"object\",\"name\":\"HelpTool\",\"id\":\"p1585\"}]}},\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1572\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1573\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1575\"},\"axis_label\":\"% Mean WT increased\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1574\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1565\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1566\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1568\"},\"axis_label\":\"Time in days\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1567\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1571\",\"attributes\":{\"axis\":{\"id\":\"p1565\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1578\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1572\"}}}]}}],\"callbacks\":{\"type\":\"map\"}}};\n  const render_items = [{\"docid\":\"cbc8ce46-4383-4c29-a889-5335e11ad457\",\"roots\":{\"p1547\":\"393b272a-792a-4619-9dc5-a5769830dc0a\"},\"root_ids\":[\"p1547\"]}];\n  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n  }\n  if (root.Bokeh !== undefined) {\n    embed_document(root);\n  } else {\n    let attempts = 0;\n    const timer = setInterval(function(root) {\n      if (root.Bokeh !== undefined) {\n        clearInterval(timer);\n        embed_document(root);\n      } else {\n        attempts++;\n        if (attempts > 100) {\n          clearInterval(timer);\n          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n        }\n      }\n    }, 10, root)\n  }\n})(window);",
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "p1547"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# A simple x y plot with a title, axis labels, and legend\n",
    "\n",
    "\n",
    "from bokeh.plotting import figure, output_file, show\n",
    "\n",
    "x = [1, 2, 3, 4, 5, 6, 7, 8]\n",
    "y = [.7, 1.4, 2.1, 3, 3.85, 4.55, 5.8, 6.45]\n",
    "\n",
    "p = figure(title='Mean wt increased vs. time',\n",
    "x_axis_label='Time in days',\n",
    "y_axis_label='% Mean WT increased')\n",
    "p.circle(x, y, size=10,) #   size: size of circle\n",
    "output_file('test.html')\n",
    "show(p)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "  <div id=\"f6cf6b2d-7753-4579-9f04-7b72eb342e61\" data-root-id=\"p1802\" style=\"display: contents;\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": "(function(root) {\n  function embed_document(root) {\n  const docs_json = {\"2a724cbb-f607-474e-a572-ec72b4dfcbe1\":{\"version\":\"3.1.0\",\"title\":\"Bokeh Application\",\"defs\":[],\"roots\":[{\"type\":\"object\",\"name\":\"Figure\",\"id\":\"p1802\",\"attributes\":{\"x_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1804\"},\"y_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1803\"},\"x_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1816\"},\"y_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1818\"},\"title\":{\"type\":\"object\",\"name\":\"Title\",\"id\":\"p1805\",\"attributes\":{\"text\":\"Mean wt increased vs. time\"}},\"renderers\":[{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1855\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1849\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1851\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1850\"},\"data\":{\"type\":\"map\",\"entries\":[[\"x\",[1,2,3,4,5,6,7,8]],[\"y\",[0.7,1.4,2.1,3,3.85,4.55,5.8,6.45]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1856\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1857\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1852\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"red\"},\"fill_color\":{\"type\":\"value\",\"value\":\"red\"},\"hatch_color\":{\"type\":\"value\",\"value\":\"red\"}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1853\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"red\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"red\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_color\":{\"type\":\"value\",\"value\":\"red\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1854\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"red\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"red\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_color\":{\"type\":\"value\",\"value\":\"red\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2}}}}},{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1864\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1858\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1860\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1859\"},\"data\":{\"type\":\"map\",\"entries\":[[\"x\",[1,2,3,4,5,6,7,8]],[\"y\",[1,2,3,4,5,6,7,8]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1865\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1866\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1861\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"blue\"},\"fill_color\":{\"type\":\"value\",\"value\":\"white\"},\"hatch_color\":{\"type\":\"value\",\"value\":\"blue\"}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1862\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"blue\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"white\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_color\":{\"type\":\"value\",\"value\":\"blue\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1863\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"size\":{\"type\":\"value\",\"value\":10},\"line_color\":{\"type\":\"value\",\"value\":\"blue\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"white\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_color\":{\"type\":\"value\",\"value\":\"blue\"},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2}}}}}],\"toolbar\":{\"type\":\"object\",\"name\":\"Toolbar\",\"id\":\"p1808\",\"attributes\":{\"tools\":[{\"type\":\"object\",\"name\":\"PanTool\",\"id\":\"p1834\"},{\"type\":\"object\",\"name\":\"WheelZoomTool\",\"id\":\"p1835\"},{\"type\":\"object\",\"name\":\"BoxZoomTool\",\"id\":\"p1836\",\"attributes\":{\"overlay\":{\"type\":\"object\",\"name\":\"BoxAnnotation\",\"id\":\"p1837\",\"attributes\":{\"syncable\":false,\"level\":\"overlay\",\"visible\":false,\"left_units\":\"canvas\",\"right_units\":\"canvas\",\"bottom_units\":\"canvas\",\"top_units\":\"canvas\",\"line_color\":\"black\",\"line_alpha\":1.0,\"line_width\":2,\"line_dash\":[4,4],\"fill_color\":\"lightgrey\",\"fill_alpha\":0.5}}}},{\"type\":\"object\",\"name\":\"SaveTool\",\"id\":\"p1838\"},{\"type\":\"object\",\"name\":\"ResetTool\",\"id\":\"p1839\"},{\"type\":\"object\",\"name\":\"HelpTool\",\"id\":\"p1840\"}]}},\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1827\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1828\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1830\"},\"axis_label\":\"% Mean WT increased\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1829\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1820\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1821\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1823\"},\"axis_label\":\"Time in days\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1822\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1826\",\"attributes\":{\"axis\":{\"id\":\"p1820\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1833\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1827\"}}}]}}],\"callbacks\":{\"type\":\"map\"}}};\n  const render_items = [{\"docid\":\"2a724cbb-f607-474e-a572-ec72b4dfcbe1\",\"roots\":{\"p1802\":\"f6cf6b2d-7753-4579-9f04-7b72eb342e61\"},\"root_ids\":[\"p1802\"]}];\n  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n  }\n  if (root.Bokeh !== undefined) {\n    embed_document(root);\n  } else {\n    let attempts = 0;\n    const timer = setInterval(function(root) {\n      if (root.Bokeh !== undefined) {\n        clearInterval(timer);\n        embed_document(root);\n      } else {\n        attempts++;\n        if (attempts > 100) {\n          clearInterval(timer);\n          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n        }\n      }\n    }, 10, root)\n  }\n})(window);",
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "p1802"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# two data series plotted on the same graph\n",
    "\n",
    "from bokeh.plotting import figure, output_file, show\n",
    "\n",
    "x = [1, 2, 3, 4, 5, 6, 7, 8]\n",
    "y = [.7, 1.4, 2.1, 3, 3.85, 4.55, 5.8, 6.45]\n",
    "y2 = [1, 2, 3, 4, 5, 6, 7, 8]\n",
    "\n",
    "p = figure(title='Mean wt increased vs. time',\n",
    "x_axis_label='Time in days',\n",
    "y_axis_label='% Mean WT increased')\n",
    "\n",
    "p.circle(x, y, size=10, color='red')\n",
    "p.circle(x, y2, size=10, color='blue', fill_color='white')\n",
    "output_file('test.html')\n",
    "show(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Chard diagram with Bokeh\n",
    "\n",
    "from bokeh.plotting import figure, output_file, show"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'Category20c' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[1;32mIn[12], line 10\u001b[0m\n\u001b[0;32m      6\u001b[0m data \u001b[39m=\u001b[39m pd\u001b[39m.\u001b[39mSeries([\u001b[39m0.1\u001b[39m, \u001b[39m0.2\u001b[39m, \u001b[39m0.3\u001b[39m, \u001b[39m0.4\u001b[39m, \u001b[39m0.5\u001b[39m, \u001b[39m0.6\u001b[39m, \u001b[39m0.7\u001b[39m, \u001b[39m0.8\u001b[39m, \u001b[39m0.9\u001b[39m, \u001b[39m1.0\u001b[39m])\u001b[39m.\u001b[39mreset_index(name\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mvalue\u001b[39m\u001b[39m'\u001b[39m)\u001b[39m.\u001b[39mrename(columns\u001b[39m=\u001b[39m{\u001b[39m'\u001b[39m\u001b[39mindex\u001b[39m\u001b[39m'\u001b[39m:\u001b[39m'\u001b[39m\u001b[39mcountry\u001b[39m\u001b[39m'\u001b[39m})\n\u001b[0;32m      8\u001b[0m data[\u001b[39m'\u001b[39m\u001b[39mangle\u001b[39m\u001b[39m'\u001b[39m] \u001b[39m=\u001b[39m data[\u001b[39m'\u001b[39m\u001b[39mvalue\u001b[39m\u001b[39m'\u001b[39m]\u001b[39m/\u001b[39mdata[\u001b[39m'\u001b[39m\u001b[39mvalue\u001b[39m\u001b[39m'\u001b[39m]\u001b[39m.\u001b[39msum()\n\u001b[1;32m---> 10\u001b[0m data[\u001b[39m'\u001b[39m\u001b[39mcolor\u001b[39m\u001b[39m'\u001b[39m] \u001b[39m=\u001b[39m Category20c[\u001b[39mlen\u001b[39m(data)]\n\u001b[0;32m     12\u001b[0m p \u001b[39m=\u001b[39m figure(height\u001b[39m=\u001b[39m\u001b[39m350\u001b[39m, title\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mPie Chart\u001b[39m\u001b[39m\"\u001b[39m, toolbar_location\u001b[39m=\u001b[39m\u001b[39mNone\u001b[39;00m,\n\u001b[0;32m     13\u001b[0m            \n\u001b[0;32m     14\u001b[0m               tools\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mhover\u001b[39m\u001b[39m\"\u001b[39m, tooltips\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m@country: @value\u001b[39m\u001b[39m\"\u001b[39m, x_range\u001b[39m=\u001b[39m(\u001b[39m-\u001b[39m\u001b[39m0.5\u001b[39m, \u001b[39m1.0\u001b[39m))\n\u001b[0;32m     16\u001b[0m p\u001b[39m.\u001b[39mwedge(x\u001b[39m=\u001b[39m\u001b[39m0\u001b[39m, y\u001b[39m=\u001b[39m\u001b[39m1\u001b[39m, radius\u001b[39m=\u001b[39m\u001b[39m0.4\u001b[39m,\n\u001b[0;32m     17\u001b[0m         start_angle\u001b[39m=\u001b[39mcumsum(\u001b[39m'\u001b[39m\u001b[39mangle\u001b[39m\u001b[39m'\u001b[39m, include_zero\u001b[39m=\u001b[39m\u001b[39mTrue\u001b[39;00m), end_angle\u001b[39m=\u001b[39mcumsum(\u001b[39m'\u001b[39m\u001b[39mangle\u001b[39m\u001b[39m'\u001b[39m),\n\u001b[0;32m     18\u001b[0m         line_color\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mwhite\u001b[39m\u001b[39m\"\u001b[39m, fill_color\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mcolor\u001b[39m\u001b[39m'\u001b[39m, source\u001b[39m=\u001b[39mdata)\n",
      "\u001b[1;31mNameError\u001b[0m: name 'Category20c' is not defined"
     ]
    }
   ],
   "source": [
    "from bokeh.plotting import figure, show\n",
    "from bokeh.models import ColumnDataSource, LabelSet\n",
    "from bokeh.transform import cumsum\n",
    "import pandas as pd\n",
    "\n",
    "data = pd.Series([0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]).reset_index(name='value').rename(columns={'index':'country'})\n",
    "\n",
    "data['angle'] = data['value']/data['value'].sum()\n",
    "\n",
    "data['color'] = Category20c[len(data)]\n",
    "\n",
    "p = figure(height=350, title=\"Pie Chart\", toolbar_location=None,\n",
    "           \n",
    "              tools=\"hover\", tooltips=\"@country: @value\", x_range=(-0.5, 1.0))\n",
    "\n",
    "p.wedge(x=0, y=1, radius=0.4,\n",
    "        start_angle=cumsum('angle', include_zero=True), end_angle=cumsum('angle'),\n",
    "        line_color=\"white\", fill_color='color', source=data)\n",
    "\n",
    "p.axis.axis_label=None\n",
    "p.axis.visible=False\n",
    "p.grid.grid_line_color = None\n",
    "\n",
    "show(p)\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       "        .bk-notebook-logo {\n",
       "            display: block;\n",
       "            width: 20px;\n",
       "            height: 20px;\n",
       "            background-image: url(data:image/png;base64,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);\n",
       "        }\n",
       "    </style>\n",
       "    <div>\n",
       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-notebook-logo\"></a>\n",
       "        <span id=\"p5497\">Loading BokehJS ...</span>\n",
       "    </div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": "(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\nconst JS_MIME_TYPE = 'application/javascript';\n  const HTML_MIME_TYPE = 'text/html';\n  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n  const CLASS_NAME = 'output_bokeh rendered_html';\n\n  /**\n   * Render data to the DOM node\n   */\n  function render(props, node) {\n    const script = document.createElement(\"script\");\n    node.appendChild(script);\n  }\n\n  /**\n   * Handle when an output is cleared or removed\n   */\n  function handleClearOutput(event, handle) {\n    const cell = handle.cell;\n\n    const id = cell.output_area._bokeh_element_id;\n    const server_id = cell.output_area._bokeh_server_id;\n    // Clean up Bokeh references\n    if (id != null && id in Bokeh.index) {\n      Bokeh.index[id].model.document.clear();\n      delete Bokeh.index[id];\n    }\n\n    if (server_id !== undefined) {\n      // Clean up Bokeh references\n      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n      cell.notebook.kernel.execute(cmd_clean, {\n        iopub: {\n          output: function(msg) {\n            const id = msg.content.text.trim();\n            if (id in Bokeh.index) {\n              Bokeh.index[id].model.document.clear();\n              delete Bokeh.index[id];\n            }\n          }\n        }\n      });\n      // Destroy server and session\n      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n      cell.notebook.kernel.execute(cmd_destroy);\n    }\n  }\n\n  /**\n   * Handle when a new output is added\n   */\n  function handleAddOutput(event, handle) {\n    const output_area = handle.output_area;\n    const output = handle.output;\n\n    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n      return\n    }\n\n    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n\n    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n      // store reference to embed id on output_area\n      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n    }\n    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n      const bk_div = document.createElement(\"div\");\n      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n      const script_attrs = bk_div.children[0].attributes;\n      for (let i = 0; i < script_attrs.length; i++) {\n        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n      }\n      // store reference to server id on output_area\n      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n    }\n  }\n\n  function register_renderer(events, OutputArea) {\n\n    function append_mime(data, metadata, element) {\n      // create a DOM node to render to\n      const toinsert = this.create_output_subarea(\n        metadata,\n        CLASS_NAME,\n        EXEC_MIME_TYPE\n      );\n      this.keyboard_manager.register_events(toinsert);\n      // Render to node\n      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n      render(props, toinsert[toinsert.length - 1]);\n      element.append(toinsert);\n      return toinsert\n    }\n\n    /* Handle when an output is cleared or removed */\n    events.on('clear_output.CodeCell', handleClearOutput);\n    events.on('delete.Cell', handleClearOutput);\n\n    /* Handle when a new output is added */\n    events.on('output_added.OutputArea', handleAddOutput);\n\n    /**\n     * Register the mime type and append_mime function with output_area\n     */\n    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n      /* Is output safe? */\n      safe: true,\n      /* Index of renderer in `output_area.display_order` */\n      index: 0\n    });\n  }\n\n  // register the mime type if in Jupyter Notebook environment and previously unregistered\n  if (root.Jupyter !== undefined) {\n    const events = require('base/js/events');\n    const OutputArea = require('notebook/js/outputarea').OutputArea;\n\n    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n      register_renderer(events, OutputArea);\n    }\n  }\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(\"p5497\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.1.0.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n          for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\nif (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(\"p5497\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));",
      "application/vnd.bokehjs_load.v0+json": ""
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Standard imports \n",
    "\n",
    "from bokeh.io import output_notebook, show\n",
    "output_notebook()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "  <div id=\"bc71668a-6200-4cf3-ad95-ca3dc079d4a6\" data-root-id=\"p5501\" style=\"display: contents;\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
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      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "p5501"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Plot a complex chart with interactive hover in a few lines of code\n",
    "\n",
    "from bokeh.models import ColumnDataSource, HoverTool\n",
    "from bokeh.plotting import figure\n",
    "from bokeh.sampledata.autompg import autompg_clean as df\n",
    "from bokeh.transform import factor_cmap\n",
    "\n",
    "df.cyl = df.cyl.astype(str)\n",
    "df.yr = df.yr.astype(str)\n",
    "\n",
    "group = df.groupby(by=['cyl', 'mfr'])\n",
    "source = ColumnDataSource(group)\n",
    "\n",
    "p = figure(width=800, height=300, title=\"Mean MPG by # Cylinders and Manufacturer\",\n",
    "           x_range=group, toolbar_location=None, tools=\"\")\n",
    "\n",
    "p.xgrid.grid_line_color = None\n",
    "p.xaxis.axis_label = \"Manufacturer grouped by # Cylinders\"\n",
    "p.xaxis.major_label_orientation = 1.2\n",
    "\n",
    "index_cmap = factor_cmap('cyl_mfr', palette=['#2b83ba', '#abdda4', '#ffffbf', '#fdae61', '#d7191c'], \n",
    "                         factors=sorted(df.cyl.unique()), end=1)\n",
    "\n",
    "p.vbar(x='cyl_mfr', top='mpg_mean', width=1, source=source,\n",
    "       line_color=\"white\", fill_color=index_cmap, \n",
    "       hover_line_color=\"darkgrey\", hover_fill_color=index_cmap)\n",
    "\n",
    "p.add_tools(HoverTool(tooltips=[(\"MPG\", \"@mpg_mean\"), (\"Cyl, Mfr\", \"@cyl_mfr\")]))\n",
    "\n",
    "show(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"900\"\n",
       "            height=\"500\"\n",
       "            src=\"https://demo.bokeh.org/sliders\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "            \n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x2278d859a90>"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Create and deploy interactive data applications\n",
    "\n",
    "from IPython.display import IFrame\n",
    "IFrame('https://demo.bokeh.org/sliders', width=900, height=500)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "IPython - 8.10.0\n",
      "Pandas - 1.5.3\n",
      "Bokeh - 3.1.0\n"
     ]
    }
   ],
   "source": [
    "from IPython import __version__ as ipython_version\n",
    "from pandas import __version__ as pandas_version\n",
    "from bokeh import __version__ as bokeh_version\n",
    "print(\"IPython - %s\" % ipython_version)\n",
    "print(\"Pandas - %s\" % pandas_version)\n",
    "print(\"Bokeh - %s\" % bokeh_version)"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
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   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
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   "name": "python",
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