Adjust igraph Layout based on "Ranked" Vertex Attribute

January 26, 2024

I have a manually created an igraph as shown below. I have created a vertex attribute labled "rank" of 1 through 4. When the I create the graph I would like the vertexes to be arranged or laid out based on those vertex attributes. So essentially the first 4 vertexes with the "rank" label of "1" would be at the top of the graph, then the single vertex with the "rank" label of "2" would be underneath the 4 vertexes with the "rank" label of "1" and so on. Is there a an argument or method in the layout to dictate location of vertex based on another column?


if (!require(librarian)){
  install.packages("librarian")
  library(librarian)
}

librarian::shelf(tidyverse, here, igraph)


g <- make_graph(~ Database+"Sierra Nevada":Panama:Brazil:Pennsylvania:Genetics:
                  "Ecophysiology & Environmental Data":eDNA:AMPs:Microbiome:"Occupancy & Abundance":Outreach:
                  Modeling:Mucosome,
                
                "Sierra Nevada"+ Genetics:"Ecophysiology & Environmental Data":eDNA:AMPs:Microbiome:
                  "Occupancy & Abundance":Outreach:Modeling:Mucosome:Database,
                
                Panama+ Genetics:"Ecophysiology & Environmental Data":eDNA:AMPs:Microbiome:
                  "Occupancy & Abundance":Outreach:Modeling:Mucosome:Database,
                
                Pennsylvania+ Genetics:"Ecophysiology & Environmental Data":eDNA:AMPs:Microbiome:
                  "Occupancy & Abundance":Outreach:Modeling:Mucosome:Database,
                
                Brazil+ Genetics:"Ecophysiology & Environmental Data":eDNA:AMPs:Microbiome:
                  "Occupancy & Abundance":Outreach:Modeling:Mucosome:Database,
                
                Genetics+ "Sierra Nevada":Panama:Brazil:Pennsylvania:Database,
                "Ecophysiology & Environmental Data"- "Sierra Nevada":Panama:Brazil:Pennsylvania:Database,
                
                eDNA+ "Sierra Nevada":Panama:Brazil:Pennsylvania:Database,
                
                AMPs+ "Sierra Nevada":Panama:Brazil:Pennsylvania:Database,
                
                Microbiome+ "Sierra Nevada":Panama:Brazil:Pennsylvania:Database,
                "Occupancy & Abundance"- "Sierra Nevada":Panama:Brazil:Pennsylvania:Database,
                
                Outreach+ "Ecophysiology & Environmental Data":AMPs:Microbiome:Mucosome:Database,
                
                Modeling+ "Sierra Nevada":Panama:Brazil:Pennsylvania:Genetics:
                  "Ecophysiology & Environmental Data":eDNA:AMPs:Microbiome:"Occupancy & Abundance":
                  Modeling:Mucosome:Database,
                
                Mucosome+ "Sierra Nevada":Panama:Brazil:Pennsylvania:Database) %>% 
  reverse_edges() %>% 
  set_vertex_attr("rank", value = c(2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 3))



plot.igraph(g, 
            layout = g$rank , 
            main = "Network",
            edge.arrow.size = 0.3,
            vertex.label.cex = 0.7, 
            #vertex.shape="none",
            edge.curved = T,
            vertex.color=as.factor(V(g)$rank))

>Solution :

There are various layout functions that can be used to affect the layout of the plot. layout_with_sugiyama() puts the nodes into different layers:

plot(g, 
     main = "Network",
     edge.arrow.size = 0.3,
     vertex.label.cex = 0.7, 
     edge.curved = TRUE,
     vertex.color=as.factor(V(g)$rank),
     layout = layout_with_sugiyama(g, layers = V(g)$rank))