Re: [igraph] Analyzing Graphs with Non-standard Node Labeling

[Gábor Csárdi]

Dear Lorenzo,

use your numbers as vertex names, i.e. use

tab <- read.table("graph_list_no_rep_dat")
g <- graph.data.frame(tab, dir=FALSE)

to create your graph. Best,
Gabor

On Wed, Jul 1, 2009 at 5:34 PM, Lorenzo Isella<address@hidden> wrote:
> Dear All,
> Consider a graph that you generate from an adjacency list but in which the
> nodes are not labeled with a standard set of integers 0,1,...... increasing
> by one for each node.
> To fix the ideas, consider the adjacency list of the graph given as
>
> 1101 1264
> 1134 1386
> 1114 1595
> 1161 1537
> 1101 1187
> 505 1138
> 1101 1114
> 1120 1138
> 501 1321
> 1132 1381
> 1138 1567
> 1197 1245
> 1118 1381
> 1499 1567
> 1101 1118
> 1002 1003
> 1197 1567
> 1167 1327
> 506 1138
> 1264 1567
> 1197 1595
> 501 1237
> 1118 1245
> 1193 1589
> 1138 1595
> 504 1167
> 1114 1567
> 1007 1524
> 1002 1237
> 1118 1514
> 1118 1264
> 506 1585
> 505 1327
> 1150 1203
> 1002 1120
> 1245 1264
> 1245 1595
> 504 1321
> 1101 1132
> 501 1120
> 1134 1203
> 1114 1187
> 1179 1196
> 1264 1611
> 1007 1578
> 1001 1002
> 1567 1595
> 1120 1264
> 1101 1245
> 506 1321
> 505 1585
> 509 1465
> 504 1120
> 1120 1245
> 1138 1237
> 1138 1585
> 1187 1381
> 506 1237
> 1264 1514
> 1386 1514
> 1245 1567
> 1237 1245
> 1132 1193
> 1101 1499
> 505 506
> 505 1120
> 502 1138
> 503 1120
> 1120 1321
> 501 1196
> 1101 1514
> 505 1321
> 1132 1187
>
> which I saved into the attached file graph_list_no_rep.dat
>
> Now, see what happens once I read and plot the graph
>
> rm(list=ls())
>
> library(Cairo)
> library(igraph)
>
>
> graph_input<-read.table("graph_list_no_rep.dat",header=FALSE)
> graph_input<-as.matrix(graph_input)
>
> graph_input_unweighted <- graph_input[ ,1:2]
>
> # Now I have the graph as a two-column matrix
>
> g <- graph(t(graph_input_unweighted), directed=FALSE)
>
> g <- simplify(g)
>
>
> #save the graph in a convenient format (e.g. edgelist)
>
> write.graph(g, "edgelist-graph", format="edgelist")
>
>
> #Now plot the graph
>
>
> E(g)$color <- "grey"
> E(g)$width <- 1
> V(g)$label.color <- "blue"
> V(g)$color  <- "SkyBlue2"
>
>
>
> pdf("network.pdf")
>
> plot(g, layout=layout.fruchterman.reingold,
>    vertex.label.dist=0.5,vertex.label=NA, vertex.size=5)
>
>
> dev.off()
>
> The generated pdf shows a graph having probably hundreds of nodes, which
> cannot be what I have in mind. The integer numbers giving the ID of each
> node are not a list where the i-th node is labeled by the integer i (or i-1
> if you count from zero), but I still would like to get a standard view of
> the graph (also for further analysis).
> How should I deal with my input file to generate the graph?
> Many thanks
>
> Lorenzo
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>



-- 
Gabor Csardi <address@hidden>     UNIL DGM