Re: [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@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

  


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and provide commented, minimal, self-contained, reproducible code.

______________________________________________
R-help@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.