[R] igraph_vertex

[Kimmo Elo]

Hi,

first of all, your example was not reproducible! But once I added
"library(igraph)" and "library(scico)" plus generally replaced
"aes_collapsed" by "edge_list", I started to work :-)

Anyway, the error is produced by this line:

+     edge.width= network,

It seems to me that you have forgotten to name a variable here (you now
use the whole network object as variable, which most probably won't
work).

Just as a kind advice for the future: if you encounter errors like
this, it is always a good idea to debug the problematic code by
commenting it out line by line. So you will - most probably - find our
those sections resulting in errors.

HTH,

Kimmo

la, 2024-02-24 kello 12:09 +0100, SIBYLLE STÖCKLI via R-help kirjoitti:
> Dear R-community
> 
>  
> 
> It would be nice to get some input how to find a solution for the
> following
> error in igraph and vertex setting.
> 
>  
> 
> Thank you very much
> 
> Sibylle
> 
>  
> 
> > par(bg="black")
> 
> > network %>% plot(
> 
> +     vertex.color=clrs[V(.)$community], 
> 
> +     vertex.size=V(.)$hub_score*1, 
> 
> +     vertex.frame.color=V(.)$color, 
> 
> +     vertex.label.color="white", 
> 
> +     vertex.label.cex=0.5, 
> 
> +     vertex.label.family="Helvetica",
> 
> +     vertex.label.font=1,
> 
> +     edge.curved=0.5,
> 
> +     edge.width= network,
> 
> +     layout=layout_with_mds(.))
> 
> Error in intI(i, n = x using Dim[1], dn[[1]], give.dn = FALSE) : 
> 
>   Index gr��er als maximales 6
> 
>  
> 
>  
> 
> Reproducible example:
> 
>  
> 
> edge_list<-read.csv("edges_table_Test.csv")
> 
>  
> 
> #create network and add some necessary attributes (vertices) for the
> plot
> 
> network <- graph_from_data_frame(aes_collapsed, directed= FALSE, 
> 
>                                  vertices = details)
> 
>  
> 
>  
> 
> temp<-cluster_optimal(network)
> 
> temp<-cbind(membership=temp$membership, Names=temp$name)
> 
> aes_collapsed <- aes_collapsed %>%
> 
>   merge(temp, by="Names")
> 
>  
> 
>  
> 
> network <- network %>%
> 
>   set_edge_attr(name = "type", value = factor(aes_collapsed$Names, 
> 
>                                                  ordered =
> is.ordered(V(network)$name))) %>%
> 
>   set_edge_attr(name = "membership", value =
> aes_collapsed$membership) %>%
> 
>   set_edge_attr(name = "color", 
> 
>               value = c(viridis::viridis(5))
> 
>               [match(E(.)$type, c(factor(V(.)$name)))]) %>%
> 
>   set_vertex_attr(name = "trans_v_net", value = c(transitivity(.,
> type =
> "local"))) %>%
> 
>   set_vertex_attr(name = "hub_score", value = c(hub_score(.)$vector))
> %>%
> 
>   set_vertex_attr(name = "color", 
> 
>               value = c(viridis::viridis((5)))
> 
>               [match(V(.)$name, c(factor(V(.)$name)))]) %>%
> 
>   set_vertex_attr(name= "community",
> value=cluster_optimal(.)$membership)
> 
>  
> 
> clrs<-scico(3, palette = "batlow")
> 
>  
> 
> par(bg="black")
> 
> network %>% plot(
> 
>      vertex.color=clrs[V(.)$community], 
> 
>      vertex.size=V(.)$hub_score*5, 
> 
>      vertex.frame.color=V(.)$color, 
> 
>      vertex.label.color="white", 
> 
>      vertex.label.cex=0.5, 
> 
>      vertex.label.family="Helvetica",
> 
>      vertex.label.font=1,
> 
>      edge.curved=0.5,
> 
>      edge.width= network,
> 
>      layout=layout_with_mds(.))
> 
>  
> 
>  
> 
> edges_table_Test.csv
> 
>  
> 
> 
> Names
> 
> target
> 
> weight
> 
> 
> B.B
> 
> A.A
> 
> 4
> 
> 
> C.C
> 
> A.A
> 
> 5
> 
> 
> D.D
> 
> A.A
> 
> 5
> 
> 
> E.E
> 
> A.A
> 
> 5
> 
> 
> F.F
> 
> A.A
> 
> 1
> 
> 
> C.C
> 
> B.B
> 
> 5
> 
> 
> E.E
> 
> B.B
> 
> 1
> 
> 
> F.F
> 
> B.B
> 
> 2
> 
> 
> A.A
> 
> C.C
> 
> 5
> 
> 
> B.B
> 
> C.C
> 
> 1
> 
> 
> D.D
> 
> C.C
> 
> 5
> 
> 
> E.E
> 
> C.C
> 
> 5
> 
> 
> F.F
> 
> C.C
> 
> 3
> 
> 
> A.A
> 
> D.D
> 
> 5
> 
> 
> B.B
> 
> D.D
> 
> 1
> 
> 
> C.C
> 
> D.D
> 
> 5
> 
> 
> E.E
> 
> D.D
> 
> 5
> 
> 
> F.F
> 
> D.D
> 
> 4
> 
> 
> A.A
> 
> E.E
> 
> 5
> 
> 
> B.B
> 
> E.E
> 
> 1
> 
> 
> C.C
> 
> E.E
> 
> 4
> 
> 
> D.D
> 
> E.E
> 
> 5
> 
> 
> F.F
> 
> E.E
> 
> 5
> 
> 
> A.A
> 
> F.F
> 
> 5
> 
> 
> B.B
> 
> F.F
> 
> 1
> 
> 
> C.C
> 
> F.F
> 
> 2
> 
> 
> D.D
> 
> F.F
> 
> 3
> 
> 
> E.E
> 
> F.F
> 
> 4
> 
> 
> F.F
> 
> F.F
> 
> 5
> 
>  
> 
> 
>         [[alternative HTML version deleted]]
> 
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