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@dgrapov dgrapov/example.R
Last active Sep 21, 2015

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Convert adjacency (or other) matrix to edge list
library(reshape2)
gen.mat.to.edge.list<-function(mat,symmetric=TRUE,diagonal=FALSE,text=FALSE){
#create edge list from matrix
# if symmetric duplicates are removed
mat<-as.matrix(mat)
id<-is.na(mat) # used to allow missing
mat[id]<-"nna"
if(symmetric){mat[lower.tri(mat)]<-"na"} # use to allow missing values
if(!diagonal){diag(mat)<-"na"}
obj<-melt(mat)
colnames(obj)<-c("source","target","value")
obj<-obj[!obj$value=="na",]
obj$value[obj$value=="nna"]<-NA
if(!text){obj$value<-as.numeric(as.character(obj$value))}
return(obj)
# remove duplicates
}
#example
R-3.1.2> x<-matrix(1:6,3,3)
R-3.1.2> x
[,1] [,2] [,3]
[1,] 1 4 1
[2,] 2 5 2
[3,] 3 6 3
#if matrix is symmetric it extracts one of the triangles (here top)
R-3.1.2> gen.mat.to.edge.list(x)
source target value
4 1 2 4
7 1 3 1
8 2 3 2
If not symmetric and you want diagonal then do the following:
R-3.1.2> gen.mat.to.edge.list(x,symmetric=FALSE,diagonal = TRUE)
source target value
1 1 1 1
2 2 1 2
3 3 1 3
4 1 2 4
5 2 2 5
6 3 2 6
7 1 3 1
8 2 3 2
9 3 3 3
#with mising values present
R-3.1.2> x[sample(1:6,3)]<-NA
R-3.1.2> x
[,1] [,2] [,3]
[1,] 1 NA 1
[2,] 2 5 2
[3,] NA NA 3
R-3.1.2> gen.mat.to.edge.list(x,symmetric=FALSE,diagonal = TRUE)
source target value
1 1 1 1
2 2 1 2
3 3 1 NA
4 1 2 NA
5 2 2 5
6 3 2 NA
7 1 3 1
8 2 3 2
9 3 3 3
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