amgen/PopulationSampling.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "outputs": [],
   "source": [
    "%matplotlib notebook\n",
    "from sym_model import Population\n",
    "import umap\n",
    "reducer = umap.UMAP()"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "outputs": [],
   "source": [
    "res = Population.random(40).sample_responses(1000)"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/lib/python3.10/site-packages/umap/umap_.py:132: UserWarning: A large number of your vertices were disconnected from the manifold.\n",
      "Disconnection_distance = inf has removed 812116 edges.\n",
      "It has fully disconnected 553 vertices.\n",
      "You might consider using find_disconnected_points() to find and remove these points from your data.\n",
      "Use umap.utils.disconnected_vertices() to identify them.\n",
      "  warn(\n",
      "/usr/lib/python3.10/site-packages/sklearn/manifold/_spectral_embedding.py:259: UserWarning: Graph is not fully connected, spectral embedding may not work as expected.\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "embedding = reducer.fit_transform(res)"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "outputs": [
    {
     "data": {
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      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.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(\n            '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\nmpl.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 = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(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 (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\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\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key
     },
     "metadata": {},
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     },
     "metadata": {},
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    }
   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "%matplotlib notebook\n",
    "plt.scatter(\n",
    "    embedding[:, 0],\n",
    "    embedding[:, 1])\n",
    "plt.show()"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "outputs": [
    {
     "data": {
      "text/plain": "(1000, 2)",
      "image/png": "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\n",
      "text/latex": "$\\displaystyle \\left( 1000, \\  2\\right)$"
     },
     "execution_count": 10,
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     "output_type": "execute_result"
    }
   ],
   "source": [
    "embedding.shape"
   ],
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    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  }
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