[R] igraph_vertex

[David Winsemius]

On 2/24/24 12:10, Kimmo Elo wrote:
> 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 :-)


After copying your lead in that replacement the error I got was:


network <- graph_from_data_frame(edge_list, directed= FALSE, + vertices 
= details) #Error: object 'details' not found Same conclusion, though. 
Incomplete presentation of code. -- David.

>
> 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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>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.