plot dendrogram with python

Jon

2007-03-27 21:38:50 UTC

Post by Frank
does anyone know if there is a way to plot a dendrogram with python.
Pylab or matplotlib do not provide such a function.

This makes a datafile for gnuplot using output from pycluster. I'd be
interested to see something like this added to pylab/matplotlib,
although I don't have time myself. Not very elegant, but someone can
probably transform it to the three line recursion which escapes me.

Best,

Jon

import Numeric
from Pycluster import treecluster
dist = Numeric.zeros((10,10),Numeric.Float)
for i in range(dist.shape[0]):
dist[i:,i:]=i

tree , dist = treecluster(distancematrix=dist,method='a')

tree=tree.tolist()
base = []
line = []
names = range(dist.shape[0]+1)

def f(i,tree,names,spos):
height=dist[spos]
if i>=0:
try:
base.append(names[i])
except:
print i
x=len(base)
line.append((x,0))
line.append((x,height))
line.append(("#","#"))
else:
cluster = tree[-i-1]
h1,x1=f(cluster[0],tree,names,-i-1)
h2,x2=f(cluster[1],tree,names,-i-1)
x=(x1+x2)/2.0
if h1==h2:
# tie
line.append((x1,h1))
line.append((x2,h2))
line.append(("#","#"))
line.append((x,height))
line.append((x,h1))
line.append(("#","#"))
else:
raise Exception("Whoops")
tree[-i-1].append((x,h1))
return height,x

h1,x1 = f(tree[-1][0],tree,names,len(tree)-1)
h2,x2 = f(tree[-1][1],tree,names,len(tree)-1)
x=(x1+x2)/2.0
height = dist[-1]
tree[-1].append((x,h1))
if h1==h2:
# tie
line.append((x1,h1))
line.append((x2,h2))
line.append(("#","#"))
line.append((x,height))
line.append((x,h1))
line.append(("#","#"))
else:
raise Exception("Whoops")

# print base

d=open("dend.dat","w")
# make a tree diagram
for point in line:
if point[0]!="#":
print >> d, point[0],point[1]
else:
print >> d
print >> d

d.close()

#
# os.system("gnuplot")
# """plot "dend.dat" u 1:2 w l"""