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