R : how to control behaviour of edges in ggraph

问题:

I'm facing this issue: I got some data like these:

library(tidyverse) library(tidygraph) library(ggraph) library(ggrepel)  edges <- data.frame(a=c('k','k','k','k','k','z','z'),                     b=c('b','b','b','b','c','b','c'), costant = 1)   a b costant 1 k b       1 2 k b       1 3 k b       1 4 k b       1 5 k c       1 6 z b       1 7 z c       1 

Now I would lik to have a graph with ggraph that have nodes and edges with weights. So I worked this way:

# first I calculated the edges weights edges1 <- edges%>% group_by(a,b) %>% summarise(weight = sum(costant)) > edges1 # A tibble: 4 x 3 # Groups:   a [?]   a     b     weight   <fct> <fct>  <dbl> 1 k     b          4 2 k     c          1 3 z     b          1 4 z     c          1 

Then the nodes:

nodes <- rbind(data.frame(word = edges$a, n = 1),data.frame(word = edges$b, n = 1)) %>%  group_by(word) %>% summarise(n = sum(n)) > nodes # A tibble: 4 x 2   word      n   <fct> <dbl> 1 k         5 2 z         2 3 b         5 4 c         2 

Till now, everything works fine. Now, following this as example:

tidy <- tbl_graph(nodes = nodes, edges = edges1, directed = T) tidy <- tidy %>%    activate(edges) %>%    arrange(desc(weight) ) 

Suddently I plotted the graph:

ggraph(tidy, layout = "gem") +    geom_node_point(aes(size=n)) +   geom_edge_link(aes(width = weight), alpha = 0.8) +    scale_edge_width(range = c(0.2, 2)) +   geom_text_repel(aes(x = x, y=y , label=word))  

But the result is this:

And I cannot figure out why there is a line between k and z, because that edges does not exists.

Thank in advance.

回答1:

It seems it's due to the fact that tbl_graph converts edge1 tibble's nodes from factor to integer by as.integer without considering the nodes tibble, this is source of the error. If we pre-convert the edge node's to integers correctly it will work as expected.

edges <- data.frame(a=c('k','k','k','k','k','z','z'),                     b=c('b','b','b','b','c','b','c'), costant = 1) edges1 <- edges%>% group_by(a,b) %>% summarise(weight = sum(costant))  nodes <- rbind(data.frame(word = edges$a, n = 1),data.frame(word = edges$b, n = 1)) %>%   group_by(word) %>%   summarise(n = sum(n))  edges2 <- edges1 # save edges with factor node labels into edge2 # convert 'from' and 'to' factor columns to integer columns correctly  # with the nodes tibble's corresponding matched index values  edges1$a <- match(edges1$a, nodes$word)  edges1$b <- match(edges1$b, nodes$word)  tidy <- tbl_graph(nodes = nodes, edges = edges1, directed = T) tidy <- tidy %>%    activate(edges) %>%    arrange(desc(weight)   )   ggraph(tidy, layout = "gem") +     geom_node_point(aes(size=n)) +    geom_edge_link(aes(width = weight), arrow = arrow(length = unit(4, 'mm')), end_cap = circle(3, 'mm'), alpha = 0.8) +     scale_edge_width(range = c(0.2, 2)) +    geom_text_repel(aes(x = x, y=y , label=word))   edges2 # compare the edges in the following tibble with the next figure # A tibble: 4 x 3 # Groups:   a [?]     a     b     weight   <fct> <fct>  <dbl> #1 k     b       4 #2 k     c       1 #3 z     b       1 #4 z     c       1 

文章来源: R : how to control behaviour of edges in ggraph