Re: [R] hc2Newick is different than th hclust dendrogram

From: Mario Valle <mvalle_at_cscs.ch>
Date: Tue, 05 Apr 2011 04:48:23 +0200

Well, I could not call them "entirely different". See attached (tree-tv from TreeView, tree-r from R).
Yes, I had to rotate and mirror the tree in TreeView but that's all. And yes, I have to ignore the tree length values from the file. Maybe it is better to post your inquiry to the Bioconductor list (from where hc2newick apparently arrives in package 'ctc'). Some humble suggestions:
- don't call a text file .Rdata! Rdata is a specific binary format read using load() and saved using save().
- add to the description of your problem how to read the data, i.e.:

z <- scan('data.Rdata')
C <- matrix(z, 112, 112, byrow=TRUE)

library('ctc')

Hope it helps

                                     mario

On 04-Apr-11 21:47, Jose Hleap Lozano wrote:
> It was... I have it in my sent box is called data.Rdata...
>
> I am attaching it again!
>
> Thanks

-- 
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82


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tree-tv.png
tree-r.png
Received on Tue 05 Apr 2011 - 02:50:33 GMT

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