Cluster plot points do not have a Y value

Question

I'm trying to understand why the output image when plotting the clusters do not have a Y value. All of the points are (x, 0). The data used in this example is a numpy array of shape (125, 532).

[[ 0.85269496  0.         -0.42126083 ... -0.09019524 -0.09706005
-0.09370346]
...
[-1.01090257  0.          0.64767467 ... -0.09020601 -0.10006334
-0.09273296]]

I'm still getting meaningful clusters so it doesn't seem to have any impact on the analysis but I'm just curious why the output is that way (if it's not just a programming mistake).

Here is the code for plotting the points. It's taken almost verbatim from the code on the scikit's page for DBSCAN.

ms = MeanShift()
X1 = StandardScaler().fit_transform(X)
ms.fit(X1)
labels = ms.labels_
unique = numpy.unique(labels)

plt.figure()
colors = [plt.cm.Spectral(each)
            for each in numpy.linspace(0, 1, len(unique))]
for k, col in zip(unique, colors):
    if k == -1:
        col = [0, 0, 0, 1]

    class_member_mask = (labels == k)

    xy = X1[class_member_mask]
    plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col), markeredgecolor='k', markersize=14)

    xy = X1[class_member_mask]
    plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col), markeredgecolor='k', markersize=6)

plt.title("Clusters")
plt.savefig(plotfn)
plt.close()

And here is the output image.

Has QUIT--Anony-Mousse · Accepted Answer · 2019-09-02 05:48:51Z

1

Supposedly your second attribute is constant 0.

In the two example rows provided it certainly is 0.

What is X1[:,1].max()? You then clearly can drop the entire column.

answered Sep 2, 2019 at 5:48

Has QUIT--Anony-Mousse

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