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vertex labels in igraph from adjacency matrix

5 messages · Mark Kimpel, Charilaos Skiadas, Gábor Csárdi

Mark Kimpel
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I am getting some unexpected results from some functions of igraph and 
it is possible that I am misinterpreting the vertex numbers. Eg., the 
max betweenness measure seems to be from a vertex that is not connected 
to a single other vertex. Below if my code snippet:

require(igraph)
my.graph <- graph.adjacency(adjmatrix = my.adj.matrix, mode=c("undirected"))

most.between.vert <- colnames(my.adj.matrix)[which(betweenness(graph = 
my.graph, v=V(my.graph), directed = FALSE) == max(betweenness(graph = 
my.graph, v=V(my.graph), directed = FALSE))) + 1]

sum(my.adj.matrix[most.between.vertext,])
0


Is there a way to automatically set the vertex name attributes from the 
row and colnames of the inputted adjacency matrix to graph.adjacency? 
This would seem like an intuitive feature, but I can't find it 
documented. In the absence of this feature, how can I make sure that I 
am setting the vertex name attributes correctly?
Charilaos Skiadas
#
On Mar 5, 2008, at 1:39 AM, Mark W Kimpel wrote:

            

      
      
      
    

        
What is the +1 for? Seems to me that this would give you the wrong  
vertex, since you find the vertex which is the max, and then you ask  
it to give you the next vertex in the list.

Btw, you will likely want to take the betweenness call out, and call  
it once and store the result, instead of calling it twice (well,  
assuming the graph is largish). Or even better, use which.max:

which.max(betweenness(graph = my.graph, v=V(my.graph), directed =  
FALSE))

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Gábor Csárdi
    

    

      
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On Wed, Mar 05, 2008 at 02:27:21AM -0500, Charilaos Skiadas wrote:

        
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This is almost good, but there is a catch, in igraph vertices are 
numbered from zero. So if you want an igraph vertex id, then you 
need to subtract one from this, i.e.:

maxb <- which.max(betweennness(my.graph, directed=FALSE))-1

You can double check it:

betweenness(my.graph, maxb, directed=FALSE)

Gabor

PS. there is also an igraph mailing list, see the igraph homepage
at igraph.sf.net

            

      
      
      
    

        
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      Gábor Csárdi
    

    

      
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Mark, graph.adjacency always preserves the order of the vertices,
so the vertex at row/column 1 will be vertex #0 in the igraph graph,
etc. I'll document this in a minute. 

This means that you can always do

g <- graph.adjacency(A)
V(g)$name <- colnames(A)

But i completely agree that this should be done by default,
i'll do that in the near future.

Btw, weighted shortest path calculation (= where the edges have 
weights or capacities) is only implemented in the development 
version of igraph. Just in case you're looking for that.

Best,
Gabor

        
On Wed, Mar 05, 2008 at 01:39:41AM -0500, Mark W Kimpel wrote:

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Mark Kimpel
    

    

      
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Looks like I turned an "off my one error" into an "off by two error" by 
adding rather than subtracting. Clearly a logic error on my part.

Also, which.max is clearly superior as it results in half as many 
function calls.

Thanks guys!

As an aside, although igraph may use the C indexing convention, R users 
and their code, is much more in tune with indexing beginning at 1. 
Adjusting this in the R interface to igraph may solve many headaches 
down the road.

Mark

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 204-4202 Home (no voice mail please)

mwkimpel<at>gmail<dot>com

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Gabor Csardi wrote: