Hi,
a quick additional note: try
"edge.width= E(.)$weight"
instead of the current "edge.width= network". Seems to work and makes
a
visible difference...
HTH,
Kimmo
su, 2024-02-25 kello 19:11 +0000, Kimmo Elo kirjoitti:>
> Hi again,
>
> your code is still not reproducible without modifications, but I
> succeed in getting the data straight. All read.csv-command are
> missing
> 'sep="\t"', it is need to read you tsv-data.
>
> And it could be more reproducible if you used e.g.
>
> --- snip ---
> aes<-read.csv(text="??? A.A?????B.B?????C.C?????D.D?????E.E?????F.F
> A.A?????0???????0???????5???????5???????5???????5
> B.B?????4???????0???????1???????1???????1???????1
> C.C?????5???????5???????0???????5???????4???????2
> D.D?????5???????0???????5???????0???????5???????3
> E.E?????5???????1???????5???????5???????0???????4
> F.F?????1???????2???????3???????4???????5???????5",?
> sep="\t", row.names = 1)
> --- snip ---
>
> This would save us from unnecessary copy-pasting :-)
>
> However, the error is still the same I mentioned in my first reply,
> i.e.:
>
> network %>% plot(
> ??? vertex.color=clrs[V(.)$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????s
> > ou
> > 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
> >
>
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