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plot dendrogram with python

P: n/a
Hi,

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

Thanks!

Frank

Mar 27 '07 #1
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P: n/a
Frank:
does anyone know if there is a way to plot a dendrogram with python.
Pylab or matplotlib do not provide such a function.
An ASCII solution:
http://aspn.activestate.com/ASPN/Coo.../Recipe/139422

Some graphics:
http://plone.org/products/phylogenetictree
http://www.bioinformatics.org/mavric/

Bye,
bearophile

Mar 27 '07 #2

P: n/a
Jon
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"""
Mar 27 '07 #4

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