igraph edges disappear when specifying vertex size

Question

Newbie to R here. I am trying to plot a network diagram with the code shown below. But when I specify the vertex size, the edges disappear. The with and without vertex specification and the resultant plot is shown below.

Without vertex size:

#NSW
clean_nsw <- clean %>% 
  filter(State=="NSW") 
clean_nsw$CountryID.Origin <- str_to_title(clean_nsw$CountryID.Origin)

nsw_plot <- graph.data.frame(d=clean_nsw, directed=T)



plot.igraph(nsw_plot,
            edge.color='grey23',
            vertex.color='deepskyblue2',
            edge.width=1,
            vertex.label.color='gray0',
            vertex.label.cex=0.75,
            vertex.label.family="Helvetica",
            vertex.label.font=2,
            arrow.width=(clean_nsw$s_count*1),
            layout= layout_nicely)

without vertex size With vertex size specified

#NSW
    clean_nsw <- clean %>% 
      filter(State=="NSW") 
    clean_nsw$CountryID.Origin <- str_to_title(clean_nsw$CountryID.Origin)

    nsw_plot <- graph.data.frame(d=clean_nsw, directed=T)



    plot.igraph(nsw_plot,
                edge.color='grey23',
                vertex.color='deepskyblue2',
                edge.width=1,
                vertex.size= clean_nsw$s_count*0.5,
                vertex.label.color='gray0',
                vertex.label.cex=0.75,
                vertex.label.family="Helvetica",
                vertex.label.font=2,
                arrow.width=(clean_nsw$s_count*1),
                layout= layout_nicely)

[image] https://i.sstatic.net/jH1oN.png

i'm not sure why when I insert the vertex size, the edges disappears. But here's the warning message that is shown:

2: In layout[, 1] + label.dist * cos(-label.degree) * (vertex.size +  :
  longer object length is not a multiple of shorter object length
3: In layout[, 2] + label.dist * sin(-label.degree) * (vertex.size +  :
  longer object length is not a multiple of shorter object length

Also, here is clean_nsw

# A tibble: 6 x 3
# Groups:   State [1]
  CountryID.Origin State s_count
  <chr>            <chr>   <int>
1 Thailand         NSW        67
2 China            NSW        51
3 Singapore        NSW        43
4 Indonesia        NSW        36
5 Fiji             NSW        32
6 Malaysia         NSW        32

Any suggestions please?

Answer 1

We can match with the attributes names of vertex and create a named vector for the vertex.size

library(igraph)
nm1 <- setNames(clean_nsw$s_count, clean_nsw$CountryID.Origin)

nm2 <-  nm1[attr(V(nsw_plot), "names")]
names(nm2)[is.na(nm2)] <- "NSW"
nm2[is.na(nm2)] <-  10 # some value
 plot.igraph(nsw_plot,
                edge.color='grey23',
                vertex.color='deepskyblue2',
                edge.width=1,
                vertex.size= nm2 * 0.5,
                        vertex.label = V(g)$names,
                vertex.label.color='gray0',
                vertex.label.cex=0.75,
                vertex.label.family="Helvetica",
                vertex.label.font=2,
                arrow.width=nm2 * 1,
                layout= layout_nicely)

-plot

data

clean_nsw <- structure(list(CountryID.Origin = c("Thailand", "China", "Singapore", 
"Indonesia", "Fiji", "Malaysia"), State = c("NSW", "NSW", "NSW", 
"NSW", "NSW", "NSW"), s_count = c(67L, 51L, 43L, 36L, 32L, 32L
)), class = "data.frame", row.names = c("1", "2", "3", "4", "5", 
"6"))