Hierarchical Clustering (Matrix Distances) View

KNIME Analytics Platform
1

Hi,

I would know if it was possible to obtain a file with the hierarchical tree on the Newick format. Or obtain the hierarchical tree in other view because, the visualize tree created by the node "Hierarchical Cluster view" is really not adapted for my work.

 

The Newick Format is :
(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0)

A,B,C,D,E are the name of the leaf and the numbers are the distances of the tree

More information on http://en.wikipedia.org/wiki/Newick_format.

 

Thanks you.

2

Do you know HiTS? It has a Dendrogram with Heatmap node in its experimental feature. Maybe it is suitable for your needs. (The experimental label is a bit odd, because it is quite stable, but when I started the distance matrix feature was only available in KNIME Labs.)

Here is a screenshot: Heatmap with Dendrogram

Hope this helps, gabor

PS.: There is also a Leaf Ordering node there which minimize the sum-difference between adjacent rows resulting an easier to follow diagram.

 

3

Thanks for this information. 
I don't think that the Heatmap will fit with my files & my boss. I need to check with him before. Maybe the leaf Ordering will help to see something in this diagram. I need to try first but I haven't the files on me....

 

Thanks you for your helps,

Gcharbonnier