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Re: [igraph] iGraph in Python: Relation between a VertexDendrogram objec

From: Tamás Nepusz
Subject: Re: [igraph] iGraph in Python: Relation between a VertexDendrogram object and VertexClustering object
Date: Tue, 2 Jul 2013 20:31:06 +0200

Hi there,

I have recently answered your question on Stack Overflow, but I'm copying my 
response here as well for the record:

"When an algorithm in igraph produces a `VertexDendrogram`, it may optionally 
produce a "hint" as well that tells us where to cut the dendrogram (i.e. after 
how many merges) to obtain a `VertexClustering` that is in some sense optimal. 
For instance, the `VertexDendrogram` produced by `community_fastgreedy()` 
proposes that the dendrogram should be cut at the point where the modularity is 
maximized. Running `as_clustering()` on a `VertexDendrogram` simply uses the 
hint produced by the clustering algorithm to flatten the dendrogram into a 
clustering, but you may override this by specifying the desired number of 
clusters as an argument to `as_clustering()`."


On 2 Jul 2013, at 18:53, "Durante, Joseph [USA]" <address@hidden> wrote:

> Hi there,
> I’m a relatively new user of iGraph and need some help with understanding a 
> function in iGraph run in Python.
> Using iGraph's community detection function community_fastgreedy(), I got a 
> VertexDendrogram object, let's call it V. Then using V.as_clustering() I got 
> a VertexClustering object from the dendrogram. I know that the communities 
> are clustered so that modularity is maximized, but I think the dendogram 
> object keeps merging all the way, so it's tough to see the communities on the 
> dendrogram.
> My question is: How does the output for the V.as_clustering() correspond to 
> distance between the communities in the dendrogram?
> In other words, The communities each come with a representative number ( 
> Community [0], Community [2] for example), so how does the that number 
> correspond to position on the dendrogram? Are community 0 and Community 1 
> adjacent to each other when the dendrogram is merged up to the level that 
> maximizes modularity, and is community 12 farther from community 0 than 3 is?
> If not, then how is the order (the numbers for each community) of the output 
> decided by the as_clustering function?
> Thanks in advance.
> -Joe
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