scipy.cluster.hierarchy: labels seems not in the r

Question

I know that scipy.cluster.hierarchy focused on dealing with the distance matrix. But now I have a similarity matrix... After I plot it by using Dendrogram, something weird just happens. Here is the code:

similarityMatrix = np.array(([1,0.75,0.75,0,0,0,0],
                         [0.75,1,1,0.25,0,0,0],
                         [0.75,1,1,0.25,0,0,0],
                         [0,0.25,0.25,1,0.25,0.25,0],
                         [0,0,0,0.25,1,1,0.75],
                         [0,0,0,0.25,1,1,0.75],
                         [0,0,0,0,0.75,0.75,1]))

here is the linkage method

Z_sim = sch.linkage(similarityMatrix)
plt.figure(1)
plt.title('similarity')
sch.dendrogram(
    Z_sim,
    labels=['1','2','3','4','5','6','7']
)
plt.show()

But here is the outcome:

My question is:

1. Why is the label for this dendrogram not right?
2. I am giving a similarity matrix for the linkage method, but I cannot fully understand what the vertical axes means. For example, as the maximum similarity is 1, why is the maximum value in the vertical axes almost 1.6?

Thank you very much for your help!

Answer 1

• linkage expects "distances", not "similarities". To convert your matrix to something like a distance matrix, you can subtract it from 1:

  dist = 1 - similarityMatrix
  

• linkage does not accept a square distance matrix. It expects the distance data to be in "condensed" form. You can get that using scipy.spatial.distance.squareform:

  from scipy.spatial.distance import squareform
  
  dist = 1 - similarityMatrix
  condensed_dist = squareform(dist)
  Z_sim = sch.linkage(condensed_dist)
  

  (When you pass a two-dimensional array with shape (m, n) to linkage, it treats the rows as points in n-dimensional space, and computes the distances internally.)