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I've created a graph from an adjacency matrix using the igraph package but I want edges to appear in the graph only when the value in the adjacency matrix is beyond a particular threshold. Using the present method I am getting all the edges which have non zero weights.

set.seed(42)
iris_matrix <- as.matrix(iris[,1:4])
image(iris_matrix)
g<-cor(iris_matrix)
library(igraph)
R<-graph.adjacency(g, mode=c("undirected"), weighted=TRUE, diag=FALSE, add.colnames=NULL, add.rownames=NULL)
plot(R)
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1 Answer 1

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Line 7 is what you need:

set.seed(42)
iris_matrix <- as.matrix(iris[,1:4])
image(iris_matrix)
g<-cor(iris_matrix)
library(igraph)
R<-graph.adjacency(g, mode=c("undirected"), weighted=TRUE, diag=FALSE, add.colnames=NULL, add.rownames=NULL)
R[R > thresh] <- 0 
plot(R)
Improve this answer
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  • $\begingroup$ Used your method @kasra manshaei but got the following error : Error in inherits(v, "igraph.vs") : (list) object cannot be coerced to type 'double' $\endgroup$
    – amankedia
    Jan 6, 2016 at 13:29
  • $\begingroup$ Check your R matrix after line 6. Whatever it is should be also after line 7 (double, int, ...). then converting it to this type will solve. Unfortunately I do not have access to R otherwise I would have sent you the code. $\endgroup$
    – Kasra Manshaei
    Jan 6, 2016 at 14:58
  • $\begingroup$ It's a 4*4 matrix @Kasra Manshaei, where do i find the 6th line :P $\endgroup$
    – amankedia
    Jan 6, 2016 at 15:05
  • $\begingroup$ :)))) I mean 6th line in the code above dude ... not inside your matrix $\endgroup$
    – Kasra Manshaei
    Jan 6, 2016 at 17:59

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