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(.)$color,
vertex.label.color="white",
vertex.label.cex=0.5,
vertex.label.family="Helvetica",
vertex.label.font=1,
edge.curved=0.5,
HERE --> edge.width= network, <-- HERE
layout=layout_with_mds(.))
Try to comment out his line and see what happens. What network data
variable should be mapped to edge width?
Best,
Kimmo
su, 2024-02-25 kello 09:59 +0100, sibylle.stoeckli at gmx.ch
kirjoitti:> Dear coummunity
>
> Thanks a lot to David and Kimmo. Yes I see now that I need to provide
> the two raw tables. Find here the reproducible example.
>
> Kind regards
> Sibylle
>
> # R-labraries
> library(circlize)
> library(ggplot2)
> library(igraph)
> library(tidyverse)
> library(RColorBrewer)
> library(stringi)
> library(scico)
> library(plotly)
> library(ggraph)
>
>
> # Tables
> aes<-read.csv("Test_adjac.csv", row.names = 1)
> details<-read.csv("Test_cat.csv")
>
> # Edge table, reorganisation
> aes_collapsed<-aes %>%
> ? rownames_to_column(var='Names') %>%
> ? tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
> ? dplyr::filter(weight != 0) %>%
> ? mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0
> negative values
>
> write.csv(aes_collapsed, "edges_table_Test.csv", row.names = F)
> edge_list<-read.csv("edges_table_Test.csv")
>
> # Network attributes
> network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
> ???????????????????????????????? vertices = details)
>
>
> temp<-cluster_optimal(network)
> temp<-cbind(membership=temp$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 at Dim[1], dn[[1]], give.dn = FALSE) :
> ? Index gr??er 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
>