{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Way number eight of looking at the correlation coefficient\n",
"\n",
"This is a notebook to accompany the blog post [\"Way number eight of looking at the correlation coefficient\"](http://composition.al/blog/2019/01/31/way-number-eight-of-looking-at-the-correlation-coefficient/). Read the post for additional context!"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from datascience import *\n",
"from datetime import *\n",
"import matplotlib\n",
"%matplotlib inline\n",
"import matplotlib.pyplot as plots\n",
"from mpl_toolkits.mplot3d import Axes3D\n",
"import pandas as pd\n",
"import math"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Recap from last time\n",
"\n",
"As [before](http://composition.al/blog/2018/08/31/understanding-the-regression-line-with-standard-units/), we're using the [datascience](http://data8.org/datascience/) package, and everything else we're using is pretty standard.\n",
"\n",
"And, as before, here's the data we'll be working with, [converted to standard units](https://www.inferentialthinking.com/chapters/14/2/Variability#standard-units) and plotted:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"
\n",
" \n",
" \n",
" Date Height (standard units) Weight (standard units) \n",
" \n",
" \n",
" \n",
" \n",
" 07/28/2017 -1.26135 -1.3158 \n",
" \n",
" \n",
" 08/07/2017 -1.08691 -1.13054 \n",
" \n",
" \n",
" 08/25/2017 -0.912464 -0.808628 \n",
" \n",
" \n",
" 09/25/2017 -0.228116 -0.399485 \n",
" \n",
" \n",
" 11/28/2017 0.107349 0.254728 \n",
" \n",
" \n",
" 01/26/2018 0.617255 0.728253 \n",
" \n",
" \n",
" 04/27/2018 1.12716 1.2537 \n",
" \n",
" \n",
" 07/30/2018 1.63707 1.41777 \n",
" \n",
" \n",
"
"
],
"text/plain": [
"Date | Height (standard units) | Weight (standard units)\n",
"07/28/2017 | -1.26135 | -1.3158\n",
"08/07/2017 | -1.08691 | -1.13054\n",
"08/25/2017 | -0.912464 | -0.808628\n",
"09/25/2017 | -0.228116 | -0.399485\n",
"11/28/2017 | 0.107349 | 0.254728\n",
"01/26/2018 | 0.617255 | 0.728253\n",
"04/27/2018 | 1.12716 | 1.2537\n",
"07/30/2018 | 1.63707 | 1.41777"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"heightweight = Table().with_columns([\n",
" 'Date', ['07/28/2017', '08/07/2017', '08/25/2017', '09/25/2017', '11/28/2017', '01/26/2018', '04/27/2018', '07/30/2018'],\n",
" 'Height (cm)', [ 53.3, 54.6, 55.9, 61, 63.5, 67.3, 71.1, 74.9],\n",
" 'Weight (kg)', [ 4.204, 4.65, 5.425, 6.41, 7.985, 9.125, 10.39, 10.785],\n",
" ])\n",
"def standard_units(nums):\n",
" return (nums - np.mean(nums)) / np.std(nums)\n",
"\n",
"heightweight_standard = Table().with_columns(\n",
" 'Date', heightweight.column('Date'),\n",
" 'Height (standard units)', standard_units(heightweight.column('Height (cm)')),\n",
" 'Weight (standard units)', standard_units(heightweight.column('Weight (kg)')))\n",
"heightweight_standard"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
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\n",
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"heightweight_standard.scatter(\n",
" 'Height (standard units)',\n",
" 'Weight (standard units)')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualizing the data in \"person space\"\n",
"\n",
"So far, this is all a recap of [last time](http://composition.al/blog/2018/08/31/understanding-the-regression-line-with-standard-units/). Now, let's try turning our data sideways.\n",
"\n",
"The hacky way I have of doing this is to convert the data first to a numpy [ndarray](https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html), then to a [pandas DataFrame](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html), and then [transposing](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.T.html#pandas.DataFrame.T) the DataFrame. This is kind of silly, but I don't know a better way to transpose a [structured ndarray](https://docs.scipy.org/doc/numpy/user/basics.rec.html). If you do, let me know."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
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"\n",
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" \n",
" \n",
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" 0 \n",
" 1 \n",
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" 3 \n",
" 4 \n",
" 5 \n",
" 6 \n",
" 7 \n",
" \n",
" \n",
" \n",
" \n",
" Date \n",
" 07/28/2017 \n",
" 08/07/2017 \n",
" 08/25/2017 \n",
" 09/25/2017 \n",
" 11/28/2017 \n",
" 01/26/2018 \n",
" 04/27/2018 \n",
" 07/30/2018 \n",
" \n",
" \n",
" Height (standard units) \n",
" -1.26135 \n",
" -1.08691 \n",
" -0.912464 \n",
" -0.228116 \n",
" 0.107349 \n",
" 0.617255 \n",
" 1.12716 \n",
" 1.63707 \n",
" \n",
" \n",
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" -1.13054 \n",
" -0.808628 \n",
" -0.399485 \n",
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" \n",
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],
"text/plain": [
" 0 1 2 3 \\\n",
"Date 07/28/2017 08/07/2017 08/25/2017 09/25/2017 \n",
"Height (standard units) -1.26135 -1.08691 -0.912464 -0.228116 \n",
"Weight (standard units) -1.3158 -1.13054 -0.808628 -0.399485 \n",
"\n",
" 4 5 6 7 \n",
"Date 11/28/2017 01/26/2018 04/27/2018 07/30/2018 \n",
"Height (standard units) 0.107349 0.617255 1.12716 1.63707 \n",
"Weight (standard units) 0.254728 0.728253 1.2537 1.41777 "
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# First convert to a plain old numpy ndarray.\n",
"heightweight_standard_np = heightweight_standard.to_array()\n",
"\n",
"# Now convert *that* to a pandas DataFrame.\n",
"df = pd.DataFrame(heightweight_standard_np)\n",
"\n",
"# Get the transpose of the DataFrame.\n",
"df = df.T\n",
"df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"pandas defaults to using `RangeIndex (0, 1, 2, …, n)` for the column labels, but we want the dates from the first row to be the column headers rather than being an actual row. That's [an easy change to make](https://stackoverflow.com/questions/26147180/convert-row-to-column-header-for-pandas-dataframe), though."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
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" \n",
" \n",
" Date \n",
" 07/28/2017 \n",
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" 08/25/2017 \n",
" 09/25/2017 \n",
" 11/28/2017 \n",
" 01/26/2018 \n",
" 04/27/2018 \n",
" 07/30/2018 \n",
" \n",
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" \n",
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"
],
"text/plain": [
"Date 07/28/2017 08/07/2017 08/25/2017 09/25/2017 \\\n",
"Height (standard units) -1.26135 -1.08691 -0.912464 -0.228116 \n",
"Weight (standard units) -1.3158 -1.13054 -0.808628 -0.399485 \n",
"\n",
"Date 11/28/2017 01/26/2018 04/27/2018 07/30/2018 \n",
"Height (standard units) 0.107349 0.617255 1.12716 1.63707 \n",
"Weight (standard units) 0.254728 0.728253 1.2537 1.41777 "
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df.columns = df.iloc[0]\n",
"df = df.drop(\"Date\")\n",
"df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"While we're at it, we'll convert the values in our DataFrame to numeric values, so that we can visualize them in a moment."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" Date \n",
" 07/28/2017 \n",
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" 08/25/2017 \n",
" 09/25/2017 \n",
" 11/28/2017 \n",
" 01/26/2018 \n",
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" \n",
" \n",
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" -1.261347 \n",
" -1.086906 \n",
" -0.912464 \n",
" -0.228116 \n",
" 0.107349 \n",
" 0.617255 \n",
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" 1.637068 \n",
" \n",
" \n",
" Weight (standard units) \n",
" -1.315798 \n",
" -1.130542 \n",
" -0.808628 \n",
" -0.399485 \n",
" 0.254728 \n",
" 0.728253 \n",
" 1.253700 \n",
" 1.417773 \n",
" \n",
" \n",
"
\n",
"
"
],
"text/plain": [
"Date 07/28/2017 08/07/2017 08/25/2017 09/25/2017 \\\n",
"Height (standard units) -1.261347 -1.086906 -0.912464 -0.228116 \n",
"Weight (standard units) -1.315798 -1.130542 -0.808628 -0.399485 \n",
"\n",
"Date 11/28/2017 01/26/2018 04/27/2018 07/30/2018 \n",
"Height (standard units) 0.107349 0.617255 1.127161 1.637068 \n",
"Weight (standard units) 0.254728 0.728253 1.253700 1.417773 "
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df = df.apply(pd.to_numeric)\n",
"df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Eight dimensions are too many to try to visualize, but we can pare it down to three. We'll pick three -- the first (07/28/2017), the last (07/30/2018), and one in the middle (01/26/2018) -- and drop the rest."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" Date \n",
" 07/28/2017 \n",
" 01/26/2018 \n",
" 07/30/2018 \n",
" \n",
" \n",
" \n",
" \n",
" Height (standard units) \n",
" -1.261347 \n",
" 0.617255 \n",
" 1.637068 \n",
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" \n",
" Weight (standard units) \n",
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"text/plain": [
"Date 07/28/2017 01/26/2018 07/30/2018\n",
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]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df_3dim = df.drop(df.columns[[1, 2, 3, 4, 6]],axis=1)\n",
"df_3dim"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we can visualize the data with a three-dimensional scatter plot."
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"application/javascript": [
"/* Put everything inside the global mpl namespace */\n",
"window.mpl = {};\n",
"\n",
"\n",
"mpl.get_websocket_type = function() {\n",
" if (typeof(WebSocket) !== 'undefined') {\n",
" return WebSocket;\n",
" } else if (typeof(MozWebSocket) !== 'undefined') {\n",
" return MozWebSocket;\n",
" } else {\n",
" alert('Your browser does not have WebSocket support.' +\n",
" 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n",
" 'Firefox 4 and 5 are also supported but you ' +\n",
" 'have to enable WebSockets in about:config.');\n",
" };\n",
"}\n",
"\n",
"mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n",
" this.id = figure_id;\n",
"\n",
" this.ws = websocket;\n",
"\n",
" this.supports_binary = (this.ws.binaryType != undefined);\n",
"\n",
" if (!this.supports_binary) {\n",
" var warnings = document.getElementById(\"mpl-warnings\");\n",
" if (warnings) {\n",
" warnings.style.display = 'block';\n",
" warnings.textContent = (\n",
" \"This browser does not support binary websocket messages. \" +\n",
" \"Performance may be slow.\");\n",
" }\n",
" }\n",
"\n",
" this.imageObj = new Image();\n",
"\n",
" this.context = undefined;\n",
" this.message = undefined;\n",
" this.canvas = undefined;\n",
" this.rubberband_canvas = undefined;\n",
" this.rubberband_context = undefined;\n",
" this.format_dropdown = undefined;\n",
"\n",
" this.image_mode = 'full';\n",
"\n",
" this.root = $('
');\n",
" this._root_extra_style(this.root)\n",
" this.root.attr('style', 'display: inline-block');\n",
"\n",
" $(parent_element).append(this.root);\n",
"\n",
" this._init_header(this);\n",
" this._init_canvas(this);\n",
" this._init_toolbar(this);\n",
"\n",
" var fig = this;\n",
"\n",
" this.waiting = false;\n",
"\n",
" this.ws.onopen = function () {\n",
" fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n",
" fig.send_message(\"send_image_mode\", {});\n",
" if (mpl.ratio != 1) {\n",
" fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n",
" }\n",
" fig.send_message(\"refresh\", {});\n",
" }\n",
"\n",
" this.imageObj.onload = function() {\n",
" if (fig.image_mode == 'full') {\n",
" // Full images could contain transparency (where diff images\n",
" // almost always do), so we need to clear the canvas so that\n",
" // there is no ghosting.\n",
" fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n",
" }\n",
" fig.context.drawImage(fig.imageObj, 0, 0);\n",
" };\n",
"\n",
" this.imageObj.onunload = function() {\n",
" fig.ws.close();\n",
" }\n",
"\n",
" this.ws.onmessage = this._make_on_message_function(this);\n",
"\n",
" this.ondownload = ondownload;\n",
"}\n",
"\n",
"mpl.figure.prototype._init_header = function() {\n",
" var titlebar = $(\n",
" '
');\n",
" var titletext = $(\n",
" '
');\n",
" titlebar.append(titletext)\n",
" this.root.append(titlebar);\n",
" this.header = titletext[0];\n",
"}\n",
"\n",
"\n",
"\n",
"mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n",
"\n",
"}\n",
"\n",
"\n",
"mpl.figure.prototype._root_extra_style = function(canvas_div) {\n",
"\n",
"}\n",
"\n",
"mpl.figure.prototype._init_canvas = function() {\n",
" var fig = this;\n",
"\n",
" var canvas_div = $('
');\n",
"\n",
" canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n",
"\n",
" function canvas_keyboard_event(event) {\n",
" return fig.key_event(event, event['data']);\n",
" }\n",
"\n",
" canvas_div.keydown('key_press', canvas_keyboard_event);\n",
" canvas_div.keyup('key_release', canvas_keyboard_event);\n",
" this.canvas_div = canvas_div\n",
" this._canvas_extra_style(canvas_div)\n",
" this.root.append(canvas_div);\n",
"\n",
" var canvas = $(' ');\n",
" canvas.addClass('mpl-canvas');\n",
" canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n",
"\n",
" this.canvas = canvas[0];\n",
" this.context = canvas[0].getContext(\"2d\");\n",
"\n",
" var backingStore = this.context.backingStorePixelRatio ||\n",
"\tthis.context.webkitBackingStorePixelRatio ||\n",
"\tthis.context.mozBackingStorePixelRatio ||\n",
"\tthis.context.msBackingStorePixelRatio ||\n",
"\tthis.context.oBackingStorePixelRatio ||\n",
"\tthis.context.backingStorePixelRatio || 1;\n",
"\n",
" mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n",
"\n",
" var rubberband = $(' ');\n",
" rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n",
"\n",
" var pass_mouse_events = true;\n",
"\n",
" canvas_div.resizable({\n",
" start: function(event, ui) {\n",
" pass_mouse_events = false;\n",
" },\n",
" resize: function(event, ui) {\n",
" fig.request_resize(ui.size.width, ui.size.height);\n",
" },\n",
" stop: function(event, ui) {\n",
" pass_mouse_events = true;\n",
" fig.request_resize(ui.size.width, ui.size.height);\n",
" },\n",
" });\n",
"\n",
" function mouse_event_fn(event) {\n",
" if (pass_mouse_events)\n",
" return fig.mouse_event(event, event['data']);\n",
" }\n",
"\n",
" rubberband.mousedown('button_press', mouse_event_fn);\n",
" rubberband.mouseup('button_release', mouse_event_fn);\n",
" // Throttle sequential mouse events to 1 every 20ms.\n",
" rubberband.mousemove('motion_notify', mouse_event_fn);\n",
"\n",
" rubberband.mouseenter('figure_enter', mouse_event_fn);\n",
" rubberband.mouseleave('figure_leave', mouse_event_fn);\n",
"\n",
" canvas_div.on(\"wheel\", function (event) {\n",
" event = event.originalEvent;\n",
" event['data'] = 'scroll'\n",
" if (event.deltaY < 0) {\n",
" event.step = 1;\n",
" } else {\n",
" event.step = -1;\n",
" }\n",
" mouse_event_fn(event);\n",
" });\n",
"\n",
" canvas_div.append(canvas);\n",
" canvas_div.append(rubberband);\n",
"\n",
" this.rubberband = rubberband;\n",
" this.rubberband_canvas = rubberband[0];\n",
" this.rubberband_context = rubberband[0].getContext(\"2d\");\n",
" this.rubberband_context.strokeStyle = \"#000000\";\n",
"\n",
" this._resize_canvas = function(width, height) {\n",
" // Keep the size of the canvas, canvas container, and rubber band\n",
" // canvas in synch.\n",
" canvas_div.css('width', width)\n",
" canvas_div.css('height', height)\n",
"\n",
" canvas.attr('width', width * mpl.ratio);\n",
" canvas.attr('height', height * mpl.ratio);\n",
" canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n",
"\n",
" rubberband.attr('width', width);\n",
" rubberband.attr('height', height);\n",
" }\n",
"\n",
" // Set the figure to an initial 600x600px, this will subsequently be updated\n",
" // upon first draw.\n",
" this._resize_canvas(600, 600);\n",
"\n",
" // Disable right mouse context menu.\n",
" $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n",
" return false;\n",
" });\n",
"\n",
" function set_focus () {\n",
" canvas.focus();\n",
" canvas_div.focus();\n",
" }\n",
"\n",
" window.setTimeout(set_focus, 100);\n",
"}\n",
"\n",
"mpl.figure.prototype._init_toolbar = function() {\n",
" var fig = this;\n",
"\n",
" var nav_element = $('
')\n",
" nav_element.attr('style', 'width: 100%');\n",
" this.root.append(nav_element);\n",
"\n",
" // Define a callback function for later on.\n",
" function toolbar_event(event) {\n",
" return fig.toolbar_button_onclick(event['data']);\n",
" }\n",
" function toolbar_mouse_event(event) {\n",
" return fig.toolbar_button_onmouseover(event['data']);\n",
" }\n",
"\n",
" for(var toolbar_ind in mpl.toolbar_items) {\n",
" var name = mpl.toolbar_items[toolbar_ind][0];\n",
" var tooltip = mpl.toolbar_items[toolbar_ind][1];\n",
" var image = mpl.toolbar_items[toolbar_ind][2];\n",
" var method_name = mpl.toolbar_items[toolbar_ind][3];\n",
"\n",
" if (!name) {\n",
" // put a spacer in here.\n",
" continue;\n",
" }\n",
" var button = $(' ');\n",
" button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +\n",
" 'ui-button-icon-only');\n",
" button.attr('role', 'button');\n",
" button.attr('aria-disabled', 'false');\n",
" button.click(method_name, toolbar_event);\n",
" button.mouseover(tooltip, toolbar_mouse_event);\n",
"\n",
" var icon_img = $(' ');\n",
" icon_img.addClass('ui-button-icon-primary ui-icon');\n",
" icon_img.addClass(image);\n",
" icon_img.addClass('ui-corner-all');\n",
"\n",
" var tooltip_span = $(' ');\n",
" tooltip_span.addClass('ui-button-text');\n",
" tooltip_span.html(tooltip);\n",
"\n",
" button.append(icon_img);\n",
" button.append(tooltip_span);\n",
"\n",
" nav_element.append(button);\n",
" }\n",
"\n",
" var fmt_picker_span = $(' ');\n",
"\n",
" var fmt_picker = $(' ');\n",
" fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');\n",
" fmt_picker_span.append(fmt_picker);\n",
" nav_element.append(fmt_picker_span);\n",
" this.format_dropdown = fmt_picker[0];\n",
"\n",
" for (var ind in mpl.extensions) {\n",
" var fmt = mpl.extensions[ind];\n",
" var option = $(\n",
" ' ', {selected: fmt === mpl.default_extension}).html(fmt);\n",
" fmt_picker.append(option)\n",
" }\n",
"\n",
" // Add hover states to the ui-buttons\n",
" $( \".ui-button\" ).hover(\n",
" function() { $(this).addClass(\"ui-state-hover\");},\n",
" function() { $(this).removeClass(\"ui-state-hover\");}\n",
" );\n",
"\n",
" var status_bar = $('');\n",
" nav_element.append(status_bar);\n",
" this.message = status_bar[0];\n",
"}\n",
"\n",
"mpl.figure.prototype.request_resize = function(x_pixels, y_pixels) {\n",
" // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n",
" // which will in turn request a refresh of the image.\n",
" this.send_message('resize', {'width': x_pixels, 'height': y_pixels});\n",
"}\n",
"\n",
"mpl.figure.prototype.send_message = function(type, properties) {\n",
" properties['type'] = type;\n",
" properties['figure_id'] = this.id;\n",
" this.ws.send(JSON.stringify(properties));\n",
"}\n",
"\n",
"mpl.figure.prototype.send_draw_message = function() {\n",
" if (!this.waiting) {\n",
" this.waiting = true;\n",
" this.ws.send(JSON.stringify({type: \"draw\", figure_id: this.id}));\n",
" }\n",
"}\n",
"\n",
"\n",
"mpl.figure.prototype.handle_save = function(fig, msg) {\n",
" var format_dropdown = fig.format_dropdown;\n",
" var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n",
" fig.ondownload(fig, format);\n",
"}\n",
"\n",
"\n",
"mpl.figure.prototype.handle_resize = function(fig, msg) {\n",
" var size = msg['size'];\n",
" if (size[0] != fig.canvas.width || size[1] != fig.canvas.height) {\n",
" fig._resize_canvas(size[0], size[1]);\n",
" fig.send_message(\"refresh\", {});\n",
" };\n",
"}\n",
"\n",
"mpl.figure.prototype.handle_rubberband = function(fig, msg) {\n",
" var x0 = msg['x0'] / mpl.ratio;\n",
" var y0 = (fig.canvas.height - msg['y0']) / mpl.ratio;\n",
" var x1 = msg['x1'] / mpl.ratio;\n",
" var y1 = (fig.canvas.height - msg['y1']) / mpl.ratio;\n",
" x0 = Math.floor(x0) + 0.5;\n",
" y0 = Math.floor(y0) + 0.5;\n",
" x1 = Math.floor(x1) + 0.5;\n",
" y1 = Math.floor(y1) + 0.5;\n",
" var min_x = Math.min(x0, x1);\n",
" var min_y = Math.min(y0, y1);\n",
" var width = Math.abs(x1 - x0);\n",
" var height = Math.abs(y1 - y0);\n",
"\n",
" fig.rubberband_context.clearRect(\n",
" 0, 0, fig.canvas.width, fig.canvas.height);\n",
"\n",
" fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n",
"}\n",
"\n",
"mpl.figure.prototype.handle_figure_label = function(fig, msg) {\n",
" // Updates the figure title.\n",
" fig.header.textContent = msg['label'];\n",
"}\n",
"\n",
"mpl.figure.prototype.handle_cursor = function(fig, msg) {\n",
" var cursor = msg['cursor'];\n",
" switch(cursor)\n",
" {\n",
" case 0:\n",
" cursor = 'pointer';\n",
" break;\n",
" case 1:\n",
" cursor = 'default';\n",
" break;\n",
" case 2:\n",
" cursor = 'crosshair';\n",
" break;\n",
" case 3:\n",
" cursor = 'move';\n",
" break;\n",
" }\n",
" fig.rubberband_canvas.style.cursor = cursor;\n",
"}\n",
"\n",
"mpl.figure.prototype.handle_message = function(fig, msg) {\n",
" fig.message.textContent = msg['message'];\n",
"}\n",
"\n",
"mpl.figure.prototype.handle_draw = function(fig, msg) {\n",
" // Request the server to send over a new figure.\n",
" fig.send_draw_message();\n",
"}\n",
"\n",
"mpl.figure.prototype.handle_image_mode = function(fig, msg) {\n",
" fig.image_mode = msg['mode'];\n",
"}\n",
"\n",
"mpl.figure.prototype.updated_canvas_event = function() {\n",
" // Called whenever the canvas gets updated.\n",
" this.send_message(\"ack\", {});\n",
"}\n",
"\n",
"// A function to construct a web socket function for onmessage handling.\n",
"// Called in the figure constructor.\n",
"mpl.figure.prototype._make_on_message_function = function(fig) {\n",
" return function socket_on_message(evt) {\n",
" if (evt.data instanceof Blob) {\n",
" /* FIXME: We get \"Resource interpreted as Image but\n",
" * transferred with MIME type text/plain:\" errors on\n",
" * Chrome. But how to set the MIME type? It doesn't seem\n",
" * to be part of the websocket stream */\n",
" evt.data.type = \"image/png\";\n",
"\n",
" /* Free the memory for the previous frames */\n",
" if (fig.imageObj.src) {\n",
" (window.URL || window.webkitURL).revokeObjectURL(\n",
" fig.imageObj.src);\n",
" }\n",
"\n",
" fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n",
" evt.data);\n",
" fig.updated_canvas_event();\n",
" fig.waiting = false;\n",
" return;\n",
" }\n",
" else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == \"data:image/png;base64\") {\n",
" fig.imageObj.src = evt.data;\n",
" fig.updated_canvas_event();\n",
" fig.waiting = false;\n",
" return;\n",
" }\n",
"\n",
" var msg = JSON.parse(evt.data);\n",
" var msg_type = msg['type'];\n",
"\n",
" // Call the \"handle_{type}\" callback, which takes\n",
" // the figure and JSON message as its only arguments.\n",
" try {\n",
" var callback = fig[\"handle_\" + msg_type];\n",
" } catch (e) {\n",
" console.log(\"No handler for the '\" + msg_type + \"' message type: \", msg);\n",
" return;\n",
" }\n",
"\n",
" if (callback) {\n",
" try {\n",
" // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n",
" callback(fig, msg);\n",
" } catch (e) {\n",
" console.log(\"Exception inside the 'handler_\" + msg_type + \"' callback:\", e, e.stack, msg);\n",
" }\n",
" }\n",
" };\n",
"}\n",
"\n",
"// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n",
"mpl.findpos = function(e) {\n",
" //this section is from http://www.quirksmode.org/js/events_properties.html\n",
" var targ;\n",
" if (!e)\n",
" e = window.event;\n",
" if (e.target)\n",
" targ = e.target;\n",
" else if (e.srcElement)\n",
" targ = e.srcElement;\n",
" if (targ.nodeType == 3) // defeat Safari bug\n",
" targ = targ.parentNode;\n",
"\n",
" // jQuery normalizes the pageX and pageY\n",
" // pageX,Y are the mouse positions relative to the document\n",
" // offset() returns the position of the element relative to the document\n",
" var x = e.pageX - $(targ).offset().left;\n",
" var y = e.pageY - $(targ).offset().top;\n",
"\n",
" return {\"x\": x, \"y\": y};\n",
"};\n",
"\n",
"/*\n",
" * return a copy of an object with only non-object keys\n",
" * we need this to avoid circular references\n",
" * http://stackoverflow.com/a/24161582/3208463\n",
" */\n",
"function simpleKeys (original) {\n",
" return Object.keys(original).reduce(function (obj, key) {\n",
" if (typeof original[key] !== 'object')\n",
" obj[key] = original[key]\n",
" return obj;\n",
" }, {});\n",
"}\n",
"\n",
"mpl.figure.prototype.mouse_event = function(event, name) {\n",
" var canvas_pos = mpl.findpos(event)\n",
"\n",
" if (name === 'button_press')\n",
" {\n",
" this.canvas.focus();\n",
" this.canvas_div.focus();\n",
" }\n",
"\n",
" var x = canvas_pos.x * mpl.ratio;\n",
" var y = canvas_pos.y * mpl.ratio;\n",
"\n",
" this.send_message(name, {x: x, y: y, button: event.button,\n",
" step: event.step,\n",
" guiEvent: simpleKeys(event)});\n",
"\n",
" /* This prevents the web browser from automatically changing to\n",
" * the text insertion cursor when the button is pressed. We want\n",
" * to control all of the cursor setting manually through the\n",
" * 'cursor' event from matplotlib */\n",
" event.preventDefault();\n",
" return false;\n",
"}\n",
"\n",
"mpl.figure.prototype._key_event_extra = function(event, name) {\n",
" // Handle any extra behaviour associated with a key event\n",
"}\n",
"\n",
"mpl.figure.prototype.key_event = function(event, name) {\n",
"\n",
" // Prevent repeat events\n",
" if (name == 'key_press')\n",
" {\n",
" if (event.which === this._key)\n",
" return;\n",
" else\n",
" this._key = event.which;\n",
" }\n",
" if (name == 'key_release')\n",
" this._key = null;\n",
"\n",
" var value = '';\n",
" if (event.ctrlKey && event.which != 17)\n",
" value += \"ctrl+\";\n",
" if (event.altKey && event.which != 18)\n",
" value += \"alt+\";\n",
" if (event.shiftKey && event.which != 16)\n",
" value += \"shift+\";\n",
"\n",
" value += 'k';\n",
" value += event.which.toString();\n",
"\n",
" this._key_event_extra(event, name);\n",
"\n",
" this.send_message(name, {key: value,\n",
" guiEvent: simpleKeys(event)});\n",
" return false;\n",
"}\n",
"\n",
"mpl.figure.prototype.toolbar_button_onclick = function(name) {\n",
" if (name == 'download') {\n",
" this.handle_save(this, null);\n",
" } else {\n",
" this.send_message(\"toolbar_button\", {name: name});\n",
" }\n",
"};\n",
"\n",
"mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {\n",
" this.message.textContent = tooltip;\n",
"};\n",
"mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Pan axes with left mouse, zoom with right\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n",
"\n",
"mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n",
"\n",
"mpl.default_extension = \"png\";var comm_websocket_adapter = function(comm) {\n",
" // Create a \"websocket\"-like object which calls the given IPython comm\n",
" // object with the appropriate methods. Currently this is a non binary\n",
" // socket, so there is still some room for performance tuning.\n",
" var ws = {};\n",
"\n",
" ws.close = function() {\n",
" comm.close()\n",
" };\n",
" ws.send = function(m) {\n",
" //console.log('sending', m);\n",
" comm.send(m);\n",
" };\n",
" // Register the callback with on_msg.\n",
" comm.on_msg(function(msg) {\n",
" //console.log('receiving', msg['content']['data'], msg);\n",
" // Pass the mpl event to the overridden (by mpl) onmessage function.\n",
" ws.onmessage(msg['content']['data'])\n",
" });\n",
" return ws;\n",
"}\n",
"\n",
"mpl.mpl_figure_comm = function(comm, msg) {\n",
" // This is the function which gets called when the mpl process\n",
" // starts-up an IPython Comm through the \"matplotlib\" channel.\n",
"\n",
" var id = msg.content.data.id;\n",
" // Get hold of the div created by the display call when the Comm\n",
" // socket was opened in Python.\n",
" var element = $(\"#\" + id);\n",
" var ws_proxy = comm_websocket_adapter(comm)\n",
"\n",
" function ondownload(figure, format) {\n",
" window.open(figure.imageObj.src);\n",
" }\n",
"\n",
" var fig = new mpl.figure(id, ws_proxy,\n",
" ondownload,\n",
" element.get(0));\n",
"\n",
" // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n",
" // web socket which is closed, not our websocket->open comm proxy.\n",
" ws_proxy.onopen();\n",
"\n",
" fig.parent_element = element.get(0);\n",
" fig.cell_info = mpl.find_output_cell(\"
\");\n",
" if (!fig.cell_info) {\n",
" console.error(\"Failed to find cell for figure\", id, fig);\n",
" return;\n",
" }\n",
"\n",
" var output_index = fig.cell_info[2]\n",
" var cell = fig.cell_info[0];\n",
"\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_close = function(fig, msg) {\n",
" var width = fig.canvas.width/mpl.ratio\n",
" fig.root.unbind('remove')\n",
"\n",
" // Update the output cell to use the data from the current canvas.\n",
" fig.push_to_output();\n",
" var dataURL = fig.canvas.toDataURL();\n",
" // Re-enable the keyboard manager in IPython - without this line, in FF,\n",
" // the notebook keyboard shortcuts fail.\n",
" IPython.keyboard_manager.enable()\n",
" $(fig.parent_element).html(' ');\n",
" fig.close_ws(fig, msg);\n",
"}\n",
"\n",
"mpl.figure.prototype.close_ws = function(fig, msg){\n",
" fig.send_message('closing', msg);\n",
" // fig.ws.close()\n",
"}\n",
"\n",
"mpl.figure.prototype.push_to_output = function(remove_interactive) {\n",
" // Turn the data on the canvas into data in the output cell.\n",
" var width = this.canvas.width/mpl.ratio\n",
" var dataURL = this.canvas.toDataURL();\n",
" this.cell_info[1]['text/html'] = ' ';\n",
"}\n",
"\n",
"mpl.figure.prototype.updated_canvas_event = function() {\n",
" // Tell IPython that the notebook contents must change.\n",
" IPython.notebook.set_dirty(true);\n",
" this.send_message(\"ack\", {});\n",
" var fig = this;\n",
" // Wait a second, then push the new image to the DOM so\n",
" // that it is saved nicely (might be nice to debounce this).\n",
" setTimeout(function () { fig.push_to_output() }, 1000);\n",
"}\n",
"\n",
"mpl.figure.prototype._init_toolbar = function() {\n",
" var fig = this;\n",
"\n",
" var nav_element = $('
')\n",
" nav_element.attr('style', 'width: 100%');\n",
" this.root.append(nav_element);\n",
"\n",
" // Define a callback function for later on.\n",
" function toolbar_event(event) {\n",
" return fig.toolbar_button_onclick(event['data']);\n",
" }\n",
" function toolbar_mouse_event(event) {\n",
" return fig.toolbar_button_onmouseover(event['data']);\n",
" }\n",
"\n",
" for(var toolbar_ind in mpl.toolbar_items){\n",
" var name = mpl.toolbar_items[toolbar_ind][0];\n",
" var tooltip = mpl.toolbar_items[toolbar_ind][1];\n",
" var image = mpl.toolbar_items[toolbar_ind][2];\n",
" var method_name = mpl.toolbar_items[toolbar_ind][3];\n",
"\n",
" if (!name) { continue; };\n",
"\n",
" var button = $(' ');\n",
" button.click(method_name, toolbar_event);\n",
" button.mouseover(tooltip, toolbar_mouse_event);\n",
" nav_element.append(button);\n",
" }\n",
"\n",
" // Add the status bar.\n",
" var status_bar = $(' ');\n",
" nav_element.append(status_bar);\n",
" this.message = status_bar[0];\n",
"\n",
" // Add the close button to the window.\n",
" var buttongrp = $('
');\n",
" var button = $(' ');\n",
" button.click(function (evt) { fig.handle_close(fig, {}); } );\n",
" button.mouseover('Stop Interaction', toolbar_mouse_event);\n",
" buttongrp.append(button);\n",
" var titlebar = this.root.find($('.ui-dialog-titlebar'));\n",
" titlebar.prepend(buttongrp);\n",
"}\n",
"\n",
"mpl.figure.prototype._root_extra_style = function(el){\n",
" var fig = this\n",
" el.on(\"remove\", function(){\n",
"\tfig.close_ws(fig, {});\n",
" });\n",
"}\n",
"\n",
"mpl.figure.prototype._canvas_extra_style = function(el){\n",
" // this is important to make the div 'focusable\n",
" el.attr('tabindex', 0)\n",
" // reach out to IPython and tell the keyboard manager to turn it's self\n",
" // off when our div gets focus\n",
"\n",
" // location in version 3\n",
" if (IPython.notebook.keyboard_manager) {\n",
" IPython.notebook.keyboard_manager.register_events(el);\n",
" }\n",
" else {\n",
" // location in version 2\n",
" IPython.keyboard_manager.register_events(el);\n",
" }\n",
"\n",
"}\n",
"\n",
"mpl.figure.prototype._key_event_extra = function(event, name) {\n",
" var manager = IPython.notebook.keyboard_manager;\n",
" if (!manager)\n",
" manager = IPython.keyboard_manager;\n",
"\n",
" // Check for shift+enter\n",
" if (event.shiftKey && event.which == 13) {\n",
" this.canvas_div.blur();\n",
" event.shiftKey = false;\n",
" // Send a \"J\" for go to next cell\n",
" event.which = 74;\n",
" event.keyCode = 74;\n",
" manager.command_mode();\n",
" manager.handle_keydown(event);\n",
" }\n",
"}\n",
"\n",
"mpl.figure.prototype.handle_save = function(fig, msg) {\n",
" fig.ondownload(fig, null);\n",
"}\n",
"\n",
"\n",
"mpl.find_output_cell = function(html_output) {\n",
" // Return the cell and output element which can be found *uniquely* in the notebook.\n",
" // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n",
" // IPython event is triggered only after the cells have been serialised, which for\n",
" // our purposes (turning an active figure into a static one), is too late.\n",
" var cells = IPython.notebook.get_cells();\n",
" var ncells = cells.length;\n",
" for (var i=0; i= 3 moved mimebundle to data attribute of output\n",
" data = data.data;\n",
" }\n",
" if (data['text/html'] == html_output) {\n",
" return [cell, data, j];\n",
" }\n",
" }\n",
" }\n",
" }\n",
"}\n",
"\n",
"// Register the function which deals with the matplotlib target/channel.\n",
"// The kernel may be null if the page has been refreshed.\n",
"if (IPython.notebook.kernel != null) {\n",
" IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n",
"}\n"
],
"text/plain": [
""
]
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"data": {
"text/html": [
" "
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""
]
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],
"source": [
"%matplotlib notebook\n",
"scatter_3d = plots.figure().gca(projection='3d')\n",
"scatter_3d.scatter(df_3dim.iloc[:, 0], df_3dim.iloc[:, 1], df_3dim.iloc[:, 2])\n",
"scatter_3d.set_xlabel(df_3dim.columns[0])\n",
"scatter_3d.set_ylabel(df_3dim.columns[1])\n",
"scatter_3d.set_zlabel(df_3dim.columns[2])\n",
"height_point = df_3dim.iloc[0]\n",
"weight_point = df_3dim.iloc[1]\n",
"origin = [0,0,0]\n",
"\n",
"X, Y, Z = zip(origin,origin) \n",
"U, V, W = zip(height_point, weight_point)\n",
"\n",
"scatter_3d.quiver(X, Y, Z, U, V, W, arrow_length_ratio=0.09)\n",
"\n",
"plots.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"What's going on here? We're in the \"person space\", where, as Rodgers and Nicewander explained, each axis represents an observation -- in this case, three observations. And there are two points, as promised -- one for each of height and weight.\n",
"\n",
"If we look at the difference between the two points on the z-axis -- that is, the axis for 07/30/2018 -- the darker-colored blue dot is higher up, so it must represent the height variable, with coordinates (-1.26135, 0.617255, 1.63707) That means that the other, lighter-colored blue dot, with coordinates (-1.3158, 0.728253, 1.41777), must represent the weight variable.\n",
"\n",
"I've also plotted vectors going from the origin to each point. These are the \"variable vectors\" for the two points."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## The angle between the variable vectors\n",
"\n",
"Finally, we want to figure out the angle between the two vectors. There are [various ways](https://stackoverflow.com/questions/2827393/angles-between-two-n-dimensional-vectors-in-python) to do that in Python; we'll use a simple one that works for us:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.11140728370937446"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"def dotproduct(v1, v2):\n",
" return sum((a*b) for a, b in zip(v1, v2))\n",
"\n",
"def length(v):\n",
" return math.sqrt(dotproduct(v, v))\n",
"\n",
"def angle(v1, v2):\n",
" return math.acos(dotproduct(v1, v2) / (length(v1) * length(v2)))\n",
"\n",
"angle_between_vvs = angle(height_point, weight_point)\n",
"angle_between_vvs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Finally, we can take the cosine of that to get the correlation coefficient $r$:"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.9938006245545371"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"math.cos(angle_between_vvs)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Almost 1! That means that, just like [last time](http://composition.al/blog/2018/08/31/understanding-the-regression-line-with-standard-units/), we have an almost perfect linear correlation.\n",
"\n",
"It's a bit different from what we had last time, though, which was 0.9910523777994954. That's because, for the sake of visualization, we decided to only look at three of the observations."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## The angle between the _actual_ variable vectors\n",
"\n",
"We can, however, go back to all eight dimensions. We may not be able to visualize them, but we can still measure the angle between them!"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.1338730551963976"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"height_point_8dim = df.iloc[0]\n",
"weight_point_8dim = df.iloc[1]\n",
"angle_between_8dim_vvs = angle(height_point_8dim, weight_point_8dim)\n",
"angle_between_8dim_vvs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Taking the cosine of this slightly bigger angle:"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.9910523777994951"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"math.cos(angle_between_8dim_vvs)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This turns out to be the same as what we had previously calculated $r$ to be, modulo a little numerical imprecision. And so, that's way number eight of looking at the correlation coefficient -- as the angle between two variable vectors in \"person space\"."
]
}
],
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"display_name": "Python 3",
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