[R] igraph_vertex
Kimmo Elo
k|mmo@e|o @end|ng |rom utu@||
Sun Feb 25 20:11:02 CET 2024
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
>
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