Some questions on dendrogram - python (Scipy)
Question: I am new to scipy but I managed to get the expected dendrogram. I am some more
questions;

  1. In the dendrogram, distance between some points are `0` but its not visible due to image border. How can I remove the border and make the lower limit of y-axis to `-1`, so that it is clearly visible. e.g. distance between these points are `0` (13,17), (2,10), (4,8,19)
  2. How can I prune/truncate on a particular distance. for e.g. prune at `0.4`
  3. How to write these clusters(after pruning) to a file

My python code:

    
    
    import scipy
    import pylab
    import scipy.cluster.hierarchy as sch
    import numpy as np
    
    D = np.genfromtxt('LtoR.txt', dtype=None)
    def llf(id):
        return str(id)
    fig = pylab.figure(figsize=(10,10))
    Y = sch.linkage(D, method='single')
    Z1 = sch.dendrogram(Y,leaf_label_func=llf,leaf_rotation=90)
    fig.show()
    fig.savefig('dendrogram.png')
    

Dendrogram: ![enter image description
here](http://i.stack.imgur.com/uumRb.png)

thank you.


Answer: 1.`fig.gca().set_ylim(-0.4,1.2)` Here `gca()` returns the current `axes`
object, so you can give it a name

    
    
    ax=fig.gca()
    ax.set_ylim(-0.4,ax.get_ylim()[1])
    

