{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Using geopandas and bokeh to create interactive world map with data" ] }, { "cell_type": "code", "execution_count": 61, "metadata": {}, "outputs": [], "source": [ "import geopandas as gpd\n", "import pandas as pd\n", "import json\n", "from bokeh.io import output_notebook, show, output_file, curdoc\n", "from bokeh.plotting import figure\n", "from bokeh.models import GeoJSONDataSource, LinearColorMapper, ColorBar, Slider, HoverTool\n", "from bokeh.palettes import brewer\n", "from bokeh.layouts import widgetbox, row, column" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Data\n", "\n", "This notebook was created using this tutorial here:[A Complete Guide to an Interactive Geographical Map using Python.](https://towardsdatascience.com/a-complete-guide-to-an-interactive-geographical-map-using-python-f4c5197e23e0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Introducing and Cleaning the Data" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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countrycountry_codegeometry
0FijiFJIMULTIPOLYGON (((180.00000 -16.06713, 180.00000...
1United Republic of TanzaniaTZAPOLYGON ((33.90371 -0.95000, 34.07262 -1.05982...
2Western SaharaSAHPOLYGON ((-8.66559 27.65643, -8.66512 27.58948...
3CanadaCANMULTIPOLYGON (((-122.84000 49.00000, -122.9742...
4United States of AmericaUSAMULTIPOLYGON (((-122.84000 49.00000, -120.0000...
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" ], "text/plain": [ " country country_code \\\n", "0 Fiji FJI \n", "1 United Republic of Tanzania TZA \n", "2 Western Sahara SAH \n", "3 Canada CAN \n", "4 United States of America USA \n", "\n", " geometry \n", "0 MULTIPOLYGON (((180.00000 -16.06713, 180.00000... \n", "1 POLYGON ((33.90371 -0.95000, 34.07262 -1.05982... \n", "2 POLYGON ((-8.66559 27.65643, -8.66512 27.58948... \n", "3 MULTIPOLYGON (((-122.84000 49.00000, -122.9742... \n", "4 MULTIPOLYGON (((-122.84000 49.00000, -120.0000... " ] }, "execution_count": 20, "metadata": {}, "output_type": "execute_result" } ], "source": [ "shapefile = 'Downloads/ne_110m_admin_0_countries/ne_110m_admin_0_countries.shp'\n", "\n", "#Read shapefile using Geopandas\n", "gdf = gpd.read_file(shapefile)[['ADMIN','ADM0_A3','geometry']]\n", "\n", "#Rename columns\n", "gdf.columns = ['country','country_code','geometry']\n", "gdf.head()" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " country country_code \\\n", "159 Antarctica ATA \n", "\n", " geometry \n", "159 MULTIPOLYGON (((-48.66062 -78.04702, -48.15140... \n" ] } ], "source": [ "print(gdf[gdf['country'] == 'Antarctica'])" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [], "source": [ "#Drop row corresponding to Antarctica\n", "gdf = gdf.drop(gdf.index[159])" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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entitycodeyearpercent_obesity
0AfghanistanAFG19750.5
1AfghanistanAFG19760.5
2AfghanistanAFG19770.6
3AfghanistanAFG19780.6
4AfghanistanAFG19790.6
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" ], "text/plain": [ " entity code year percent_obesity\n", "0 Afghanistan AFG 1975 0.5\n", "1 Afghanistan AFG 1976 0.5\n", "2 Afghanistan AFG 1977 0.6\n", "3 Afghanistan AFG 1978 0.6\n", "4 Afghanistan AFG 1979 0.6" ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "datafile = 'Datasets/share-of-adults-defined-as-obese.csv'\n", "\n", "#Read csv file using pandas\n", "df = pd.read_csv(datafile, names=['entity','code','year','percent_obesity'], skiprows=1)\n", "\n", "df.head()" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "RangeIndex: 8316 entries, 0 to 8315\n", "Data columns (total 4 columns):\n", " # Column Non-Null Count Dtype \n", "--- ------ -------------- ----- \n", " 0 entity 8316 non-null object \n", " 1 code 7980 non-null object \n", " 2 year 8316 non-null int64 \n", " 3 percent_obesity 8316 non-null float64\n", "dtypes: float64(1), int64(1), object(2)\n", "memory usage: 260.0+ KB\n" ] } ], "source": [ "df.info()" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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entitycodeyearpercent_obesity
42AfricaNaN19752.0
43AfricaNaN19762.1
44AfricaNaN19772.2
45AfricaNaN19782.3
46AfricaNaN19792.3
...............
8185Western PacificNaN20125.2
8186Western PacificNaN20135.5
8187Western PacificNaN20145.8
8188Western PacificNaN20156.1
8189Western PacificNaN20166.4
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336 rows × 4 columns

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" ], "text/plain": [ " entity code year percent_obesity\n", "42 Africa NaN 1975 2.0\n", "43 Africa NaN 1976 2.1\n", "44 Africa NaN 1977 2.2\n", "45 Africa NaN 1978 2.3\n", "46 Africa NaN 1979 2.3\n", "... ... ... ... ...\n", "8185 Western Pacific NaN 2012 5.2\n", "8186 Western Pacific NaN 2013 5.5\n", "8187 Western Pacific NaN 2014 5.8\n", "8188 Western Pacific NaN 2015 6.1\n", "8189 Western Pacific NaN 2016 6.4\n", "\n", "[336 rows x 4 columns]" ] }, "execution_count": 25, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df[df.code.isnull()]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Static choropleth map for 2016" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [], "source": [ "#Filter data for year 2016\n", "df_2016 = df[df['year'] == 2016]\n", "\n", "#Merge dataframes gdf and df_2016\n", "merged = gdf.merge(df_2016, left_on='country_code', right_on='code')" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [], "source": [ "#Read data to json\n", "merged_json = json.loads(merged.to_json())\n", "\n", "#Convert to String like object\n", "json_data = json.dumps(merged_json)" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var 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", "\n", " var JS_MIME_TYPE = 'application/javascript';\n", " var HTML_MIME_TYPE = 'text/html';\n", " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", " var CLASS_NAME = 'output_bokeh rendered_html';\n", "\n", " /**\n", " * Render data to the DOM node\n", " */\n", " function render(props, node) {\n", " var 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", " var cell = handle.cell;\n", "\n", " var id = cell.output_area._bokeh_element_id;\n", " var 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", " var cmd = \"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, {\n", " iopub: {\n", " output: function(msg) {\n", " var 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", " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", " cell.notebook.kernel.execute(cmd);\n", " }\n", " }\n", "\n", " /**\n", " * Handle when a new output is added\n", " */\n", " function handleAddOutput(event, handle) {\n", " var output_area = handle.output_area;\n", " var output = handle.output;\n", "\n", " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", " if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", " return\n", " }\n", "\n", " var 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", " var bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " var script_attrs = bk_div.children[0].attributes;\n", " for (var 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", " var 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", " var 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", " var events = require('base/js/events');\n", " var 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", "\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", " var NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\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", " \"

\\n\"+\n", " \"\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " var el = document.getElementById(\"1652\");\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", "\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() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\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", " const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n", "\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " if (url in hashes) {\n", " element.crossOrigin = \"anonymous\";\n", " element.integrity = \"sha384-\" + hashes[url];\n", " }\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", " \n", " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n", " var css_urls = [];\n", " \n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " function(Bokeh) {\n", " \n", " \n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if (root.Bokeh !== undefined || force === true) {\n", " \n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " if (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", " var cell = $(document.getElementById(\"1652\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\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": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var 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\n \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 var NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\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 \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
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10.760000000000002]]]}}]}\",\"selected\":{\"id\":\"1711\"},\"selection_policy\":{\"id\":\"1712\"}},\"id\":\"1611\",\"type\":\"GeoJSONDataSource\"},{\"attributes\":{\"axis\":{\"id\":\"1625\"},\"grid_line_color\":null,\"ticker\":null},\"id\":\"1628\",\"type\":\"Grid\"},{\"attributes\":{\"source\":{\"id\":\"1611\"}},\"id\":\"1651\",\"type\":\"CDSView\"},{\"attributes\":{\"high\":40,\"low\":0,\"palette\":[\"#ffffd9\",\"#edf8b1\",\"#c7e9b4\",\"#7fcdbb\",\"#41b6c4\",\"#1d91c0\",\"#225ea8\",\"#0c2c84\"]},\"id\":\"1612\",\"type\":\"LinearColorMapper\"},{\"attributes\":{\"data_source\":{\"id\":\"1611\"},\"glyph\":{\"id\":\"1648\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"1649\"},\"selection_glyph\":null,\"view\":{\"id\":\"1651\"}},\"id\":\"1650\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"axis\":{\"id\":\"1629\"},\"dimension\":1,\"grid_line_color\":null,\"ticker\":null},\"id\":\"1632\",\"type\":\"Grid\"},{\"attributes\":{},\"id\":\"1630\",\"type\":\"BasicTicker\"},{\"attributes\":{\"active_drag\":\"auto\",\"active_inspect\":\"auto\",\"active_multi\":null,\"active_scroll\":\"auto\",\"active_tap\":\"auto\",\"tools\":[{\"id\":\"1633\"},{\"id\":\"1634\"},{\"id\":\"1635\"},{\"id\":\"1636\"},{\"id\":\"1637\"},{\"id\":\"1638\"}]},\"id\":\"1640\",\"type\":\"Toolbar\"},{\"attributes\":{},\"id\":\"1634\",\"type\":\"WheelZoomTool\"},{\"attributes\":{},\"id\":\"1705\",\"type\":\"BasicTickFormatter\"},{\"attributes\":{},\"id\":\"1633\",\"type\":\"PanTool\"},{\"attributes\":{},\"id\":\"1712\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"overlay\":{\"id\":\"1639\"}},\"id\":\"1635\",\"type\":\"BoxZoomTool\"},{\"attributes\":{},\"id\":\"1636\",\"type\":\"SaveTool\"},{\"attributes\":{\"color_mapper\":{\"id\":\"1612\"},\"formatter\":{\"id\":\"1707\"},\"height\":20,\"label_standoff\":8,\"location\":[0,0],\"major_label_overrides\":{\"0\":\"0%\",\"10\":\"10%\",\"15\":\"15%\",\"20\":\"20%\",\"25\":\"25%\",\"30\":\"35%\",\"40\":\">40%\",\"5\":\"5%\"},\"orientation\":\"horizontal\",\"ticker\":{\"id\":\"1706\"},\"width\":500},\"id\":\"1613\",\"type\":\"ColorBar\"},{\"attributes\":{},\"id\":\"1711\",\"type\":\"Selection\"},{\"attributes\":{},\"id\":\"1706\",\"type\":\"BasicTicker\"},{\"attributes\":{},\"id\":\"1707\",\"type\":\"BasicTickFormatter\"},{\"attributes\":{},\"id\":\"1709\",\"type\":\"BasicTickFormatter\"}],\"root_ids\":[\"1614\"]},\"title\":\"Bokeh Application\",\"version\":\"2.2.3\"}};\n", " var render_items = [{\"docid\":\"ecaf4648-bb49-4bee-b4ed-04930b9df4e6\",\"root_ids\":[\"1614\"],\"roots\":{\"1614\":\"f700c8f4-5c2a-4058-9270-758ea7b72887\"}}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", "\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " var attempts = 0;\n", " var 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": "1614" } }, "output_type": "display_data" } ], "source": [ "#Import GeoJSON source that contains features for plotting\n", "geosource = GeoJSONDataSource(geojson = json_data)\n", "\n", "#Define a sequential multi-hue color palette\n", "palette = brewer['YlGnBu'][8]\n", "\n", "#Reverse color order so that dark blue is highest obesity\n", "palette = palette[::-1]\n", "\n", "#Instantiate LinearColorMapper that linearly maps numbers in a range into a sequence of colors\n", "color_mapper = LinearColorMapper(palette=palette, low=0, high=40)\n", "\n", "#Define custom tick labels for color bar\n", "tick_labels = {'0':'0%','5':'5%','10':'10%','15':'15%','20':'20%','25':'25%','30':'30%','30':'35%','40':'>40%'}\n", "\n", "#Create color bar\n", "color_bar = ColorBar(color_mapper=color_mapper, label_standoff=8, width=500, height=20, \n", " border_line_color=None, location=(0,0), orientation='horizontal',\n", " major_label_overrides=tick_labels)\n", "\n", "#Create figure object\n", "fig = figure(title='Share of adults who are obese, 2016', plot_height=600, plot_width=950, toolbar_location=None)\n", "fig.xgrid.grid_line_color=None\n", "fig.ygrid.grid_line_color=None\n", "\n", "#Add patch renderer to figure\n", "fig.patches('xs', 'ys', source=geosource, fill_color={'field': 'percent_obesity', 'transform': color_mapper},\n", " line_color='black', line_width=0.25, fill_alpha=1)\n", "\n", "#Specify figure layout\n", "fig.add_layout(color_bar, 'below')\n", "\n", "#Display figure inline in Jupyter Notebook\n", "output_notebook()\n", "\n", "#Display figure\n", "show(fig)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Including missing countries" ] }, { "cell_type": "code", "execution_count": 39, "metadata": {}, "outputs": [], "source": [ "#Perform left merge to preserve every row in gdf\n", "merged = gdf.merge(df_2016, left_on='country_code', right_on='code', how='left')" ] }, { "cell_type": "code", "execution_count": 40, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var 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", "\n", " var JS_MIME_TYPE = 'application/javascript';\n", " var HTML_MIME_TYPE = 'text/html';\n", " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", " var CLASS_NAME = 'output_bokeh rendered_html';\n", "\n", " /**\n", " * Render data to the DOM node\n", " */\n", " function render(props, node) {\n", " var 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", " var cell = handle.cell;\n", "\n", " var id = cell.output_area._bokeh_element_id;\n", " var 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", " var cmd = \"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, {\n", " iopub: {\n", " output: function(msg) {\n", " var 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", " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", " cell.notebook.kernel.execute(cmd);\n", " }\n", " }\n", "\n", " /**\n", " * Handle when a new output is added\n", " */\n", " function handleAddOutput(event, handle) {\n", " var output_area = handle.output_area;\n", " var output = handle.output;\n", "\n", " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", " if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", " return\n", " }\n", "\n", " var 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", " var bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " var script_attrs = bk_div.children[0].attributes;\n", " for (var 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", " var 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", " var 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? 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\\n\"+\n", " \"

\\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", " \"

\\n\"+\n", " \"\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " var el = document.getElementById(\"1804\");\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", "\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() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\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", " const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n", "\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " if (url in hashes) {\n", " element.crossOrigin = \"anonymous\";\n", " element.integrity = \"sha384-\" + hashes[url];\n", " }\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", " \n", " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n", " var css_urls = [];\n", " \n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " function(Bokeh) {\n", " \n", " \n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if (root.Bokeh !== undefined || force === true) {\n", " \n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " if (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", " var cell = $(document.getElementById(\"1804\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\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": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var 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\n \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 var NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\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 \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
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4.249884947362048], [33.3900000000001, 3.7899999999999636], [32.686420000000055, 3.7923200000000747], [31.881449999999973, 3.558269999999993], [31.24556000000007, 3.7819000000000074], [30.833852421715427, 3.5091716042224625]]]}}]}\",\"selected\":{\"id\":\"1873\"},\"selection_policy\":{\"id\":\"1874\"}},\"id\":\"1763\",\"type\":\"GeoJSONDataSource\"}],\"root_ids\":[\"1766\"]},\"title\":\"Bokeh Application\",\"version\":\"2.2.3\"}};\n", " var render_items = [{\"docid\":\"d9de1146-2c60-4882-8bf5-d27847d95c4a\",\"root_ids\":[\"1766\"],\"roots\":{\"1766\":\"1985381d-dd9f-4328-96c4-f2eb5319c2e2\"}}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", "\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " var attempts = 0;\n", " var 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": "1766" } }, "output_type": "display_data" } ], "source": [ "#Read data to json\n", "merged_json = json.loads(merged.to_json())\n", "\n", "#Convert to String like object\n", "json_data = json.dumps(merged_json)\n", "\n", "#Import GeoJSON source that contains features for plotting\n", "geosource = GeoJSONDataSource(geojson = json_data)\n", "\n", "#Instantiate LinearColorMapper that linearly maps numbers in a range into a sequence of colors\n", "color_mapper = LinearColorMapper(palette=palette, low=0, high=40)\n", "\n", "#Create figure object\n", "fig = figure(title='Share of adults who are obese, 2016', plot_height=600, plot_width=950, toolbar_location=None)\n", "fig.xgrid.grid_line_color=None\n", "fig.ygrid.grid_line_color=None\n", "\n", "#Add patch renderer to figure\n", "fig.patches('xs', 'ys', source=geosource, fill_color={'field': 'percent_obesity', 'transform': color_mapper},\n", " line_color='black', line_width=0.25, fill_alpha=1)\n", "\n", "#Specify figure layout\n", "fig.add_layout(color_bar, 'below')\n", "\n", "#Display figure inline in Jupyter Notebook\n", "output_notebook()\n", "\n", "#Display figure\n", "show(fig)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Correcting for missing countries" ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "outputs": [], "source": [ "#Replace NaN values to string \"No Data\"\n", "merged.fillna(\"No Data\", inplace=True)" ] }, { "cell_type": "code", "execution_count": 42, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
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\\n\"+\n", " \"

\\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", " \"

\\n\"+\n", " \"\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " var el = document.getElementById(\"1965\");\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", "\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() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\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", " const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n", "\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " if (url in hashes) {\n", " element.crossOrigin = \"anonymous\";\n", " element.integrity = \"sha384-\" + hashes[url];\n", " }\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", " \n", " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n", " var css_urls = [];\n", " \n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " function(Bokeh) {\n", " \n", " \n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if (root.Bokeh !== undefined || force === true) {\n", " \n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " if (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", " var cell = $(document.getElementById(\"1965\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\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": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var 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\n \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 var NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\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 \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n var el = document.getElementById(\"1965\");\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\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() {\n console.error(\"failed to load \" + url);\n }\n\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\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 const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n if (url in hashes) {\n element.crossOrigin = \"anonymous\";\n element.integrity = \"sha384-\" + hashes[url];\n }\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 \n var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n var css_urls = [];\n \n\n var inline_js = [\n function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\n function(Bokeh) {\n \n \n }\n ];\n\n function run_inline_js() {\n \n if (root.Bokeh !== undefined || force === true) {\n \n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n if (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 var cell = $(document.getElementById(\"1965\")).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\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));" }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
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of adults who are obese, 2016\"},\"id\":\"1928\",\"type\":\"Title\"},{\"attributes\":{},\"id\":\"2038\",\"type\":\"BasicTickFormatter\"},{\"attributes\":{\"fill_color\":{\"field\":\"percent_obesity\",\"transform\":{\"id\":\"1926\"}},\"line_width\":{\"value\":0.25},\"xs\":{\"field\":\"xs\"},\"ys\":{\"field\":\"ys\"}},\"id\":\"1961\",\"type\":\"Patches\"},{\"attributes\":{},\"id\":\"2045\",\"type\":\"UnionRenderers\"}],\"root_ids\":[\"1927\"]},\"title\":\"Bokeh Application\",\"version\":\"2.2.3\"}};\n", " var render_items = [{\"docid\":\"92c504fd-ef5f-4f74-a42d-ceafe21aa783\",\"root_ids\":[\"1927\"],\"roots\":{\"1927\":\"8aac6758-968b-4a6b-b0db-bb59b3c6472e\"}}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", "\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " var attempts = 0;\n", " var 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": "1927" } }, "output_type": "display_data" } ], "source": [ "#Read data to json\n", "merged_json = json.loads(merged.to_json())\n", "\n", "#Convert to String like object\n", "json_data = json.dumps(merged_json)\n", "\n", "#Import GeoJSON source that contains features for plotting\n", "geosource = GeoJSONDataSource(geojson = json_data)\n", "\n", "#Instantiate LineaerColorMapper that maps numbers in a range linearly into a sequence of colors. Input nan_color.\n", "color_mapper = LinearColorMapper(palette=palette, low=0, high=40, nan_color = '#d9d9d9')\n", "\n", "#Create figure object\n", "fig = figure(title='Share of adults who are obese, 2016', plot_height=600, plot_width=950, toolbar_location=None)\n", "fig.xgrid.grid_line_color=None\n", "fig.ygrid.grid_line_color=None\n", "\n", "#Add patch renderer to figure\n", "fig.patches('xs', 'ys', source=geosource, fill_color={'field': 'percent_obesity', 'transform': color_mapper},\n", " line_color='black', line_width=0.25, fill_alpha=1)\n", "\n", "#Specify figure layout\n", "fig.add_layout(color_bar, 'below')\n", "\n", "#Display figure inline in Jupyter Notebook\n", "output_notebook()\n", "\n", "#Display figure\n", "show(fig)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Adding interactivity" ] }, { "cell_type": "code", "execution_count": 65, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "BokehDeprecationWarning: 'WidgetBox' is deprecated and will be removed in Bokeh 3.0, use 'bokeh.models.Column' instead\n" ] }, { "data": { "text/html": [ "\n", "
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3.5091716042224625]]]}}]}\",\"selected\":{\"id\":\"7069\"},\"selection_policy\":{\"id\":\"7070\"}},\"id\":\"6762\",\"type\":\"GeoJSONDataSource\"},{\"attributes\":{},\"id\":\"7068\",\"type\":\"BasicTickFormatter\"},{\"attributes\":{\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"field\":\"percent_obesity\",\"transform\":{\"id\":\"2689\"}},\"line_alpha\":{\"value\":0.1},\"line_width\":{\"value\":0.25},\"xs\":{\"field\":\"xs\"},\"ys\":{\"field\":\"ys\"}},\"id\":\"6787\",\"type\":\"Patches\"},{\"attributes\":{\"active_drag\":\"auto\",\"active_inspect\":\"auto\",\"active_multi\":null,\"active_scroll\":\"auto\",\"active_tap\":\"auto\",\"tools\":[{\"id\":\"6763\"}]},\"id\":\"6783\",\"type\":\"Toolbar\"},{\"attributes\":{\"text\":\"Share of adults who are obese, 2016\"},\"id\":\"6765\",\"type\":\"Title\"},{\"attributes\":{\"color_mapper\":{\"id\":\"2689\"},\"formatter\":{\"id\":\"2841\"},\"height\":20,\"label_standoff\":8,\"location\":[0,0],\"major_label_overrides\":{\"0\":\"0%\",\"10\":\"10%\",\"15\":\"15%\",\"20\":\"20%\",\"25\":\"25%\",\"30\":\"30%\",\"35\":\"35%\",\"40\":\">40%\",\"5\":\"5%\"},\"orientation\":\"horizontal\",\"ticker\":{\"id\":\"2840\"},\"width\":500},\"id\":\"2691\",\"type\":\"ColorBar\"},{\"attributes\":{},\"id\":\"2841\",\"type\":\"BasicTickFormatter\"}],\"root_ids\":[\"6764\"]},\"title\":\"Bokeh Application\",\"version\":\"2.2.3\"}};\n", " var render_items = [{\"docid\":\"2402b808-de65-4a1c-95bc-7275f74c5c98\",\"root_ids\":[\"6764\"],\"roots\":{\"6764\":\"e60b94ba-2f42-4244-b50e-13501f681e01\"}}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", "\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " var attempts = 0;\n", " var 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": "6764" } }, "output_type": "display_data" } ], "source": [ "#Define function that returns json_data for year selected by user\n", "def json_data(selectedYear):\n", " yr = selectedYear\n", " df_yr = df[df['year'] == yr]\n", " merged = gdf.merge(df_yr, left_on='country_code', right_on='code', how='left')\n", " merged.fillna('No Data', inplace=True)\n", " merged_json = json.loads(merged.to_json())\n", " json_data = json.dumps(merged_json)\n", " return json_data\n", "\n", "#Input GeoJSON source that contains features for plotting\n", "geosource = GeoJSONDataSource(geojson = json_data(2016))\n", "\n", "#Add hover tool\n", "hover = HoverTool(tooltips = [('Country/region', '@country'), ('%obesity', '@percent_obesity')])\n", "\n", "#Create figure object\n", "fig = figure(title='Share of adults who are obese, 2016', plot_height=600, plot_width=950, toolbar_location=None,\n", " tools=[hover])\n", "fig.xgrid.grid_line_color=None\n", "fig.ygrid.grid_line_color=None\n", "\n", "#Add patch renderer to figure\n", "fig.patches('xs', 'ys', source=geosource, fill_color={'field': 'percent_obesity', 'transform': color_mapper},\n", " line_color='black', line_width=0.25, fill_alpha=1)\n", "\n", "#Specify figure layout\n", "fig.add_layout(color_bar, 'below')\n", "\n", "#Define the callback function: update_plot\n", "def update_plot(attr, old, new):\n", " yr = slider.value\n", " new_data = json_data(yr)\n", " geosource.geojson = new_data\n", " fig.title.text = 'Share of adults who are obese, %d %yr'\n", " \n", "#Make a slider object: slider\n", "slider = Slider(title='Year', start=1975, end=2016, step=1, value=2016)\n", "slider.on_change('value', update_plot)\n", "\n", "#Make a column layout of widgetbox(slider) and plot, and add it to the current document\n", "layout = column(fig, widgetbox(slider))\n", "curdoc().add_root(layout)\n", "\n", "#Display figure inline in Jupyter Notebook\n", "output_notebook()\n", "\n", "#Display figure\n", "show(fig)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Viewing in Interactive Mode\n", "\n", "To view the interactive map on the local host, run the code in this Notebook on local device and type `bokeh serve --show filename.ipynb` into the local terminal. A local host page will open up in the browser with the interactive widget bar and map." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "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": "3.8.5" } }, "nbformat": 4, "nbformat_minor": 4 }