docs/tutorials/embedding/forceatlas.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# ForceAtlas\n",
    "\n",
    "This notebook illustrates the embedding of a graph through the force-directed algorithm Force Atlas 2.\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.display import SVG"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sknetwork.data import karate_club\n",
    "from sknetwork.embedding.force_atlas import ForceAtlas\n",
    "from sknetwork.visualization import svg_graph"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Example"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "graph = karate_club(metadata=True)\n",
    "adjacency = graph.adjacency\n",
    "labels = graph.labels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
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      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "forceatlas2 = ForceAtlas()\n",
    "embedding = forceatlas2.fit_transform(adjacency)\n",
    "image = svg_graph(adjacency, embedding, labels=labels)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Options"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we illustrate the influences of the different settings offered to the user."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Replace the linear attraction force with a logarithmic attraction force."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
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      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "forceatlas2 = ForceAtlas(lin_log = True)\n",
    "embedding = forceatlas2.fit_transform(adjacency)\n",
    "image = svg_graph(adjacency, embedding, labels=labels)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Set the gravity and repulsion force constants (`gravity_factor` and `repulsion_factor`)\n",
    "to set the importance of each force in the layout. Keep values between 0.01 and 0.1."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
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      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "forceatlas2 = ForceAtlas(gravity_factor = 0.1)\n",
    "embedding = forceatlas2.fit_transform(adjacency)\n",
    "image = svg_graph(adjacency, embedding, labels=labels)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Set the amount of swinging tolerated. Lower swinging yields less speed and more precision."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
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      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "forceatlas2 = ForceAtlas(tolerance=1.5)\n",
    "embedding = forceatlas2.fit_transform(adjacency)\n",
    "image = svg_graph(adjacency, embedding, labels=labels)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
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      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "forceatlas2 = ForceAtlas(approx_radius=2)\n",
    "embedding = forceatlas2.fit_transform(adjacency)\n",
    "image = svg_graph(adjacency, embedding, labels=labels)\n",
    "SVG(image)"
   ]
  }
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