Visualize High-Dimensional Network Data with 3D Scatter Plot

3DScatterGraph-2.py

def ThreeDplot(model):
    
    "Creates TSNE model and plots it"
    "Get the labels and vectors from ndoe2vec mode"
    labels = []
    tokens = []

    for word in model.wv.vocab:
        tokens.append(model[word])
        labels.append(word)
    
    "Index the label table and prepare for annotating the graph" 
    lab = []
    for i in labels:
      lab.append(label[label.Vertex==i].values[0][1])
    
    "make a tsne model, set n_components = 3 which will reduce the size of dimensions to 3."
    tsne_model = TSNE(perplexity=10, n_components=3, learning_rate=20, init='random', n_iter=1000, random_state=42)
    new_values = tsne_model.fit_transform(tokens)

    x = []
    y = []
    z = []
    for value in new_values:
        x.append(value[0])
        y.append(value[1])
        z.append(value[2])
    
    "create 3D scatter plot with seaborn and matlibplot"
    sns.set_style("whitegrid", {'axes.grid' : False})

    fig = plt.figure(figsize=(20, 15))

    ax = Axes3D(fig) 

    gist_ncar = cm.get_cmap('gist_ncar', len(set(lab)))

    ax.scatter(x, y, z, c=lab, cmap=gist_ncar, marker='o',alpha=0.7,s=200)
    ax.set_xlabel('X Label')
    ax.set_ylabel('Y Label')
    ax.set_zlabel('Z Label')

    "annotating the graph"
    for x_label, y_label, z_label, label_node in zip(x, y, z, lab):
      ax.text(x_label, y_label, z_label, label_node)

    ## 360 degree view
    def rotate(angle):
      ax.view_init(azim=angle)

    "configure paths, specifically for Google Colab; use 'pillow' as writer instead of 'imagemagick' "
    rc('animation', html='jshtml')
    rot_animation = animation.FuncAnimation(fig, rotate, frames=np.arange(0,362,2),interval=100)
    rot_animation.save('rotation.gif', dpi=40, writer='pillow') 
    rot_animation