So I’ve been through a few hours of searching + trial & error and came up with a simple solution to draw an animated GIF 3D scatterplot.
(minimum library installs, exclude bash commands)
X = data.iloc[:,0:-1] Y = data.iloc[:,-1].astype('int') from sklearn.manifold import TSNE tsne = TSNE(n_components=3, random_state=RS, perplexity=10) tsne_fit = tsne.fit_transform(X)
n_components should be set to 3 in order to draw a 3D plot.
perpliexity should be adjusted by trial and error to find the best value that represents your data.
sqrt(N) is a good starting point.
from mpl_toolkits.mplot3d import Axes3D from matplotlib import animation fig = plt.figure(figsize=(10,10)) ax = Axes3D(fig) colors = 'b', 'r' labels = 'Group1', 'Group2' for i, c, label in zip(range(len(labels)), colors, labels): ax.scatter(tsne_fit[data['Group']==i, 0], tsne_fit[data['Group']==i, 1], tsne_fit[data['Group']==i, 2], s=30, c=c, label=label, alpha=0.5) fig.legend()
Axes3D is for 3D plotting.
matplotlib.animation is for making animated GIF.
Draw the scatterplot. In my case, I used scatter() twice to label the outcome feature.
alpha=0.5 for better visualization when datapoints overlap.
def rotate(angle): ax.view_init(azim=angle) angle = 3 ani = animation.FuncAnimation(fig, rotate, frames=np.arange(0, 360, angle), interval=50) ani.save('inhadr_tsne1.gif', writer=animation.PillowWriter(fps=20))
Build an arbitrary function
rotate() that updates the view of the plot. This function will be called by
The writer is set to
PillowWriter since it’s included by default in matplotlib. But while searching, I found that in some cases there are some problems in the animation, and can be solved by using a different writer, such as
angle=3 means the plot rotates 3 degrees every frame. (120 frames in total)
fps=20 values can be tweaked to change the rotation speed of animation.
Took 10 seconds to draw this.
대만족! This is definitely going to be put in my next presentation!
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