[R] igraph_vertex

[Kimmo Elo]

Hi again,

your code is still not reproducible without modifications, but I
succeed in getting the data straight. All read.csv-command are missing
'sep="\t"', it is need to read you tsv-data.

And it could be more reproducible if you used e.g.

--- snip ---
aes<-read.csv(text="    A.A	B.B	C.C	D.D	E.E	F.F
A.A	0	0	5	5	5	5
B.B	4	0	1	1	1	1
C.C	5	5	0	5	4	2
D.D	5	0	5	0	5	3
E.E	5	1	5	5	0	4
F.F	1	2	3	4	5	5", 
sep="\t", row.names = 1)
--- snip ---

This would save us from unnecessary copy-pasting :-)

However, the error is still the same I mentioned in my first reply,
i.e.:

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,
HERE -->    edge.width= network,  <-- HERE
    layout=layout_with_mds(.))

Try to comment out his line and see what happens. What network data
variable should be mapped to edge width?

Best,
Kimmo

su, 2024-02-25 kello 09:59 +0100, sibylle.stoeckli using gmx.ch kirjoitti:
> Dear coummunity
> 
> Thanks a lot to David and Kimmo. Yes I see now that I need to provide
> the two raw tables. Find here the reproducible example.
> 
> Kind regards
> Sibylle
> 
> # R-labraries
> library(circlize)
> library(ggplot2)
> library(igraph)
> library(tidyverse)
> library(RColorBrewer)
> library(stringi)
> library(scico)
> library(plotly)
> library(ggraph)
> 
> 
> # Tables
> aes<-read.csv("Test_adjac.csv", row.names = 1)
> details<-read.csv("Test_cat.csv")
> 
> # Edge table, reorganisation
> aes_collapsed<-aes %>%
>   rownames_to_column(var='Names') %>%
>   tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
>   dplyr::filter(weight != 0) %>%
>   mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0 =
> negative values
> 
> write.csv(aes_collapsed, "edges_table_Test.csv", row.names = F)
> edge_list<-read.csv("edges_table_Test.csv")
> 
> # Network attributes
> 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(.))
> 
> #error
> Error in intI(i, n = x using Dim[1], dn[[1]], give.dn = FALSE) : 
>   Index größer als maximales 6
> 
> # Test_adjac.csv
>         A.A     B.B     C.C     D.D     E.E     F.F
> A.A     0       0       5       5       5       5
> B.B     4       0       1       1       1       1
> C.C     5       5       0       5       4       2
> D.D     5       0       5       0       5       3
> E.E     5       1       5       5       0       4
> F.F     1       2       3       4       5       5
> 
> # Test_cat.csv
> Names   corresponding-
> NCP       Category        Subcategory_type        sources.cyto    sou
> rce  Factor
> A.A     7       hydrologic attribute            "A"     A       1
> B.B     6, 11   hydrologic attribute            "B"     B       1
> C.C     1, 14, 15, 16, 17,
> 18   AES     intrinsic       "C"     C       0
> D.D     1, 14, 15, 16, 17,
> 18   AES     intrinsic       "D"     D       0
> E.E     1, 14, 15, 16, 17,
> 18   AES     intrinsic       "E"     E       0
> F.F     7       AES     material        "F"     F       0
> 
> 
> # edges_tables_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
>