rigraphggnetwork

remove unconnected nodes R igraph or ggnet

I have a symmetric matrix that represent degree of connections among actors. I would like to cancel out the vertex unconnected.

The functions included in igraph (as delete_edges or delete_vertices) do not work for my case. I share my code

#import of matrix
matrix3<-import("matrix2a.xlsx")
r.name <- matrix2a [,1]
rownames(matrix2a) <- r.name
matrix2a <- matrix2a %>% select(-X__1)
View(matrix2a)
m=as.matrix(matrix2a)
#I compute the maximum spanning tree graph
g <- graph_from_adjacency_matrix(m, mode = "upper", weighted = T, diag = F)
max_spann_tree <- mst(g, weights = -E(g)$weight)
#I obtain a network with some unconneted vertex that I would like to erase

thanks in advance for your help!

Solution

  • I am not sure what you mean "The functions included in igraph (as delete_edges or delete_vertices) do not work for my case." delete.vertices is made for precisely this purpose.

    Since you do not provide data, I will show a small example from random data. I am adding labels to the graph so that the numbering will not change when I delete the isolated vertices. I am also using an explicit layout so I can lay out the reduced graph in the same way for comparison. 

    library(igraph)
set.seed(1234)
G = erdos.renyi.game(40, 0.055)
V(G)$label=1:40     
LO = layout_with_fr(G)
plot(G, layout = LO)

    Graph 01

    Now identify the isolated vertices and use delete.vertices to remove them.

    Isolated = which(degree(G)==0)
G2 = delete.vertices(G, Isolated)
LO2 = LO[-Isolated,]
plot(G2, layout=LO2)

    Graph 02

    The same graph but without the isolated vertices.

    If this is not what you want, please be more explicit about why it does not work for your graph.