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Hi , How can i specify a cutoff for the algorithm , #21
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Dear Lars, Thank you very much for your reply : The code bellow is line 92 of HierarchyBuilder.agglomerate(): Distance newDistance = linkageStrategy.calculateDistance(distanceValues);
} iam sorry iam confused , how can i specify the cutoff , the code above is : producing a linkage proximity matrix, i change the code Distance newDistance = linkageStrategy.calculateDistance(distanceValues); newLinkage.setLinkageDistance(newDistance.setDistance(0.5)); it does not work , the error is : Void not allowed Please need your guidance. Best On Mon, Sep 12, 2016 at 10:58 AM, Lars Behnke [email protected]
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Pls give a reply Ibehnke |
Here is a figure on this home page: https://github.com/lbehnke/hierarchical-clustering-java. From this dendrogram, how can we get clusters or groups. For example, if we want get two clusters, it should be [o6] [o1 o2 o3 o4 o5]; If we want get three clusters, it should be [06] [03 05] [01 02 04 ]. How to use codes to get such clusters and output them to console or files? Thanks! |
In my case, I have more than 800 samples/genes. After clustering, the dendrogram is very big and complex, therfore, we need to divide/cut/sect the dendrogram into clusters and save them to files (each file contains the gene names and represents a cluster/group). |
I have test the algorithm on my dataset , the distance height is between 0,1. for example it assign 0, 0, 0 , 0 then the rest are 1.
the distance is a matrix from euclidean distance method .
then if would like cut the tree when distances = 0.5 ?? how can i do that , distances is [][] symatrics matrix.
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