Does this shape has two clusters or one?

Question

This cluster belongs to the direction of one side group from a long peptide during the simulation. I tried to make each cluster has its own color by those lines, Does that right?
mds = manifold.MDS(max_iter=200, eps=1e-4, n_init=1,dissimilarity='precomputed',random_state=0)
dp_mds = mds.fit_transform(distance)
t = np.arange(2000)
plt.scatter(dp_mds[:, 0], dp_mds[:, 1], c=t)

Does this shape two clusters or one?

gringer · Answer

It's hard to know without more information.
Dimensional reduction is a tool to improve the visual understandability of a dataset, but it shouldn't be used as the primary information for determining clusters in the data. There's no general way to look at a reduced-dimensionality image and from that image alone work out the clustered nature of a higher-order dataset.

Does this shape has two clusters or one?

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