# Generate synthetic dataset dataset = make_trefoil(size=100) X = dataset.data y = dataset.target # Generate shape graph using KeplerMapper mapper = KeplerMapper(verbose=1) lens = mapper.fit_transform(X, projection=[0]) graph = mapper.map(lens, X, nr_cubes=6, overlap_perc=0.2) # Convert to a DyNeuGraph dG = DyNeuGraph(G=graph, y=y) # Define some custom_layouts dG.add_custom_layout(lens, name='lens') dG.add_custom_layout(nx.spring_layout, name='nx.spring') dG.add_custom_layout(nx.kamada_kawai_layout, name='nx.kamada_kawai') dG.add_custom_layout(nx.spectral_layout, name='nx.spectral') dG.add_custom_layout(nx.circular_layout, name='nx.circular') # Configure some projections pca = PCA(2, random_state=1) tsne = TSNE(2, init='pca', random_state=1) umap = UMAP(n_components=2, init=pca.fit_transform(X)) # Add projections as custom_layouts dG.add_custom_layout(pca.fit_transform(X), name='PCA') dG.add_custom_layout(tsne.fit_transform(X), name='TSNE') dG.add_custom_layout(umap.fit_transform(X, y=None), name='UMAP')
X = masker.fit_transform(dataset.func[0])
# Encode labels as integers
df = pd.read_csv(dataset.session_target[0], sep=" ")
target, labels = pd.factorize(df.labels.values)
y = pd.DataFrame({l:(target==i).astype(int) for i,l in enumerate(labels)})
# Generate shape graph using KeplerMapper
mapper = KeplerMapper(verbose=1)
lens = mapper.fit_transform(X, projection=TSNE(2, random_state=1))
graph = mapper.map(
lens, X=X,
cover=Cover(20, 0.5),
clusterer=DBSCAN(eps=20.)
)
dG = DyNeuGraph(G=graph, y=y)
# Define some custom_layouts
import networkx as nx
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
dG.add_custom_layout(nx.spring_layout, name='nx.spring')
dG.add_custom_layout(nx.kamada_kawai_layout, name='nx.kamada_kawai')
dG.add_custom_layout(nx.spectral_layout, name='nx.spectral')
dG.add_custom_layout(nx.circular_layout, name='nx.circular')
dG.add_custom_layout(PCA(2).fit_transform(X), name='PCA')
dG.add_custom_layout(TSNE(2).fit_transform(X), name='TSNE')
# Visualize
dG.visualize('dyneusr_custom_layouts.html', static=True, show=True)