title: How to get flat clustering corresponding to color clusters in the dendrogram created by scipy
body: <p>Using the code posted <a href="https://stackoverflow.com/questions/2455761/reordering-matrix-elements-to-reflect-column-and-row-clustering-in-naiive-python/3017704#3017704">here</a>, I created a nice hierarchical clustering:</p>
  
  <p><img src="https://i.stack.imgur.com/hj00i.png" alt="scipy dendrogram"></p>
  
  <p>Let's say the the dendrogram on the left was created by doing something like</p>
  
  <pre><code>Y = sch.linkage(D, method='average') # D is a distance matrix
  cutoff = 0.5*max(Y[:,2])
  Z = sch.dendrogram(Y, orientation='right', color_threshold=cutoff)
  </code></pre>
  
  <p>Now <strong>how do I get the indices of the members of each of the colored clusters?</strong>  To simplify this situation, ignore the clustering on the top, and focus only on the dendrogram on the left of the matrix.</p>
  
  <p>This information should be stored in the dendrogram <code>Z</code> stored variable.  There is a function that should do just what I want called <code>fcluster</code> (see documentation <a href="http://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.fcluster.html#scipy.cluster.hierarchy.fcluster" rel="noreferrer">here</a>). However I cannot see where I can give fcluster the same <code>cutoff</code> as I specified in the creation of the dendrogram.  It seems that the threshold variable in <code>fcluster</code>, <code>t</code> has to be in terms of various obscure measurements (<code>inconsistent</code>, <code>distance</code>, <code>maxclust</code>, <code>monocrit</code>).  Any ideas? </p>