[R] geom_edge & color

[Kimmo Elo]

Dear Sibylle,

your example is not working! E.g. no data for "aes_collapsed".

Best,

Kimmo

ke, 2024-03-20 kello 19:28 +0100, SIBYLLE STÖCKLI via R-help kirjoitti:
> Dear community
> 
> I am using ggraph to plot a network analysis. See part 2 in the working
> example.
> Besides different colors for different groups of nodes:
> --> geom_node_point(aes(size = V(network)$hub_score*200, color=
> as.factor(V(network)$community)))
> I additionally want to consider different colors for different edge
> groups
> The grouping is defined in the edge_list$relationship: negative
> relationship
> = red and positive relationship = darkblue. The code is working in the
> way
> that the  groups are separated by two colors. However, the code uses not
> the
> assigned colors. Does anyone have any idea how to adapt the code?
> --> geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10),
> color=c("darkblue", "red")[as.factor(edge_list$relationship)],
> alpha=0.5)) +
> 
> Kind regards
> Sibylle
> 
> 
> 
> 
> Working example
> 
> library(circlize)
> library(ggplot2)
> library(igraph)
> library(tidyverse)
> library(RColorBrewer)
> library(stringi)
> library(scico)
> library(plotly)
> library(ggraph)
> 
> edges_table_Test.csv
> 
> Names   target  weight relationship
> B.B     A.A     4           pos
> C.C     A.A     5           pos
> D.D     A.A     5           neg
> E.E     A.A     5          neg
> F.F     A.A     1          pos
> C.C     B.B     5         pos
> E.E     B.B     1           pos
> F.F     B.B     2          pos
> A.A     C.C     5        pos
> B.B     C.C     1        pos
> D.D     C.C     5         pos
> E.E     C.C     5         pos
> F.F     C.C     3         pos
> A.A     D.D     5        neg
> B.B     D.D     1        neg
> C.C     D.D     5        neg
> E.E     D.D     5        neg
> F.F     D.D     4         neg
> A.A     E.E     5         neg
> B.B     E.E     1        neg
> C.C     E.E     4        neg
> D.D     E.E     5        neg
> F.F     E.E     5       pos
> A.A     F.F     5        pos
> B.B     F.F     1       pos
> C.C     F.F     2       pos
> D.D     F.F     3      pos
> E.E     F.F     4       pos
> F.F     F.F     5       pos
> 
> edge_list<-read.csv("edges_table_Test.csv")
> 
> network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
>                                  vertices = details)
> 
> temp<-cluster_optimal(network)
> temp<-cbind(membership=temp$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")
> 
> ### part 1: network plot
> par(bg="black")
> network %>% plot(
>      vertex.color=clrs[V(.)$community],
>      vertex.size=V(.)$hub_score*5,
>      vertex.frame.color=V(.)$color,
>      vertex.label.color="white",
>      vertex.label.cex=0.5,
>      vertex.label.family="Helvetica",
>      vertex.label.font=1,
>      edge.curved=0.5,
>      edge.width= network,
>      layout=layout_with_mds(.))
> 
> ### part 2: ggraph
> tiff("figures/AES_network_bymembership.tiff", width=1000, height=700,
> res=120) network %>%
>   ggraph(., layout = "auto")+
> geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10),
> color=c("darkblue", "red")[as.factor(edge_list$relationship)],
> alpha=0.5)) +
> 
>   geom_node_point(aes(size = V(network)$hub_score*200, color=
> as.factor(V(network)$community))) +
>   geom_node_text(aes(label =  V(network)$name), size=5, color="white",
> repel=T)+
>   scale_color_scico_d(palette = "batlow")+
>   scale_edge_width(range = c(0.2,4))+
>   scale_size(range = c(0.5,20)) +
>   #scale_edge_color_manual(values = c(scico(21, palette="batlow")))+
>   theme(plot.background = element_rect(fill = "black"),
>         legend.position = "right",
>         panel.background = element_rect(fill = "black"))
> dev.off()
> 
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