{
"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 visualize_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": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"forceatlas2 = ForceAtlas()\n",
"embedding = forceatlas2.fit_transform(adjacency)\n",
"image = visualize_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": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"forceatlas2 = ForceAtlas(lin_log = True)\n",
"embedding = forceatlas2.fit_transform(adjacency)\n",
"image = visualize_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": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 37,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"forceatlas2 = ForceAtlas(gravity_factor = 0.1)\n",
"embedding = forceatlas2.fit_transform(adjacency)\n",
"image = visualize_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": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 41,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"forceatlas2 = ForceAtlas(tolerance=1.5)\n",
"embedding = forceatlas2.fit_transform(adjacency)\n",
"image = visualize_graph(adjacency, embedding, labels=labels)\n",
"SVG(image)"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 42,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"forceatlas2 = ForceAtlas(approx_radius=2)\n",
"embedding = forceatlas2.fit_transform(adjacency)\n",
"image = visualize_graph(adjacency, embedding, labels=labels)\n",
"SVG(image)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.9.13"
}
},
"nbformat": 4,
"nbformat_minor": 4
}