On index attribute in ggraph

Question

I’ m using ggraph to plot graphs based on hierarchical edge bundling. I’m using the example from https://www.r-graph-gallery.com/311-add-labels-to-hierarchical-edge-bundling.html. I have a question about the significance of index in the network representation? Can we replace the color of the links with another attribute?

The code:

library(ggraph)
library(igraph)
library(tidyverse)
library(RColorBrewer)

# create a data frame giving the hierarchical structure of your individuals
set.seed(1234)
d1 <- data.frame(from="origin", to=paste("group", seq(1,10), sep=""))
d2 <- data.frame(from=rep(d1$to, each=10), to=paste("subgroup", seq(1,100), sep="_"))
edges <- rbind(d1, d2)

# create a dataframe with connection between leaves (individuals)
all_leaves <- paste("subgroup", seq(1,100), sep="_")
connect <- rbind( 
  data.frame( from=sample(all_leaves, 100, replace=T) , to=sample(all_leaves, 100, replace=T)), 
  data.frame( from=sample(head(all_leaves), 30, replace=T) , to=sample( tail(all_leaves), 30, replace=T)), 
  data.frame( from=sample(all_leaves[25:30], 30, replace=T) , to=sample( all_leaves[55:60], 30, replace=T)), 
  data.frame( from=sample(all_leaves[75:80], 30, replace=T) , to=sample( all_leaves[55:60], 30, replace=T)) )
connect$value <- runif(nrow(connect))

# create a vertices data.frame. One line per object of our hierarchy
vertices  <-  data.frame(
  name = unique(c(as.character(edges$from), as.character(edges$to))) , 
  value = runif(111)
) 
# Let's add a column with the group of each name. It will be useful later to color points
vertices$group  <-  edges$from[ match( vertices$name, edges$to ) ]
#Let's add information concerning the label we are going to add: angle, horizontal adjustement and potential flip
#calculate the ANGLE of the labels
vertices$id <- NA
myleaves <- which(is.na( match(vertices$name, edges$from) ))
nleaves <- length(myleaves)
vertices$id[ myleaves ] <- seq(1:nleaves)
vertices$angle <- 90 - 360 * vertices$id / nleaves

# calculate the alignment of labels: right or left
# If I am on the left part of the plot, my labels have currently an angle < -90
vertices$hjust <- ifelse( vertices$angle < -90, 1, 0)

# flip angle BY to make them readable
vertices$angle <- ifelse(vertices$angle < -90, vertices$angle+180, vertices$angle)
# Create a graph object
mygraph <- igraph::graph_from_data_frame( edges, vertices=vertices )

# The connection object must refer to the ids of the leaves:
from  <-  match( connect$from, vertices$name)
to  <-  match( connect$to, vertices$name)
ggraph(mygraph, layout = 'dendrogram', circular = TRUE) + 
  geom_conn_bundle(data = get_con(from = from, to = to), alpha=0.2, width=0.9, aes(colour=..index..)) +
  scale_edge_colour_distiller(palette = "RdPu") +
  
  geom_node_text(aes(x = x*1.15, y=y*1.15, filter = leaf, label=name, angle = angle, hjust=hjust, colour=group), size=2, alpha=1) +
  
  geom_node_point(aes(filter = leaf, x = x*1.07, y=y*1.07, colour=group, size=value, alpha=0.2)) +
  scale_colour_manual(values= rep( brewer.pal(9,"Paired") , 30)) +
  scale_size_continuous( range = c(0.1,10) )

AugtPelle · Answer 1 · 2022-02-07T17:26:48.863

You can specify the attributes directly like this:

ggraph(mygraph, layout = 'dendrogram', circular = TRUE) + 
  geom_conn_bundle(data = get_con(from = from, to = to), alpha=0.2, width=0.9, aes(colour=x)) +
  scale_edge_colour_distiller(palette = "RdPu")

The same for y. You can also change the the parameter using the dots after and before the variable: ..x.. or ..y..

Update:

# The connection object must refer to the ids of the leaves:
from  <-  match( connect$from, vertices$name)
to  <-  match( connect$to, vertices$name)
value  <-  match( connect$value, vertices$name)
ggraph(mygraph, layout = 'dendrogram', circular = TRUE) + 
  geom_conn_bundle(data = get_con(from = from, to = to, vakue = value), alpha=0.2, width=0.9, 
                   aes(colour=..value..)) +
  scale_edge_colour_distiller(palette = "RdPu") +
  
  geom_node_text(aes(x = x*1.15, y=y*1.15, filter = leaf, label=name, angle = angle, hjust=hjust, colour=group), size=2, alpha=1) +
  
  geom_node_point(aes(filter = leaf, x = x*1.07, y=y*1.07, colour=group, size=value, alpha=0.2)) +
  scale_colour_manual(values= rep( brewer.pal(9,"Paired") , 30)) +
  scale_size_continuous( range = c(0.1,10) )

@AugtPette, thank you for your reply. Actually, I want the color of the links to be from connect$value but I cannot select this attribute. — user1988, Feb 07 '22 at 17:02
Let me know if the update works. In this case, the graphs connections change due to the amount of values we are adding. — AugtPelle, Feb 07 '22 at 17:27
I am facing the same issue: conect$value is not selectable. In the example at https://r-graph-gallery.com/310-custom-hierarchical-edge-bundling.html the coloring comes from vertices$value. How can I fix that? best regards, Christoph — Chris_hro, Jun 08 '23 at 15:40

On index attribute in ggraph

1 Answers1