[SciPy-Dev] Hiearchical Clustering issue
Rishabh SHARMA
rishabh.sharma.gunner at gmail.com
Wed Mar 4 12:15:58 EST 2015
hey Richard
This works as a charm.
Thanks
Rishabh
On Wed, Mar 4, 2015 at 10:21 PM, Richard Tsai <richard9404 at gmail.com> wrote:
> Hi Rishabh,
>
> hierarchy.linkage requires its first argument to be a *condensed* distance
> matrix, which can be obtained using some functions in spatial.distance. If
> a 2d array is provided, it will be considered as an observation vectors
> array. Check the docs here
> http://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage
>
> Regards,
> Richard
>
> > 在 2015年3月4日,20:56,Rishabh SHARMA <rishabh.sharma.gunner at gmail.com> 写道:
> >
> > Hello
> > I have this question,could someone help?
> >
> > I am using scipy.cluster.hiearchical
> > ***I have a distance matrix in squareform 't' as
> > array([[ 0.00000000e+00, 3.44600000e+03, 6.75000000e+02,
> > 2.06000000e+03, 2.24205600e+06],
> > [ 3.44600000e+03, 0.00000000e+00, 2.77300000e+03,
> > 1.75000000e+03, 2.23959500e+06],
> > [ 6.75000000e+02, 2.77300000e+03, 0.00000000e+00,
> > 1.49100000e+03, 2.24154200e+06],
> > [ 2.06000000e+03, 1.75000000e+03, 1.49100000e+03,
> > 0.00000000e+00, 2.24127000e+06],
> > [ 2.24205600e+06, 2.23959500e+06, 2.24154200e+06,
> > 2.24127000e+06, 0.00000000e+00]])
> >
> > ***I used this cmd
> > z=linkage(t,method='complete') //t is the above matrix
> > z
> > array([[ 0.00000000e+00, 2.00000000e+00, 1.39718861e+03,
> > 2.00000000e+00],
> > [ 1.00000000e+00, 3.00000000e+00, 3.53484724e+03,
> > 2.00000000e+00],
> > [ 5.00000000e+00, 6.00000000e+00, 5.85696654e+03,
> > 4.00000000e+00],
> > [ 4.00000000e+00, 7.00000000e+00, 5.00927065e+06,
> > 5.00000000e+00]])
> >
> > **Question: why in the first row of z where objects 0,2 are merged the
> > distance is shown as 1.397e+3[3rd element of 1st row] whereas it should
> > the distance given by t[0][2] as in distance matrix(these objects are
> > original objects/leaf nodes)
> >
> > Thanks
> >
> >
> > PS: I posted the question in user list,but no one seems to have the
> answer.In any case sorry for spamming dev list.
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>
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