Smooth transitions between different layouts of the same network in ggraph

Question

I would like to animate the same network using different layouts and having a smooth transition between layouts. I'd like to do this inside the gganimate framework.

library(igraph)
library(ggraph)
library(gganimate)

set.seed(1)
g <- erdos.renyi.game(10, .5, "gnp")
V(g)$name <- letters[1:vcount(g)]
l1 <- create_layout(g, "kk")
l2 <- create_layout(g, "circle")
l3 <- create_layout(g, "nicely")
long <- rbind(l1,l2,l3)
long$frame <- rep(1:3, each =10)

Following the ggplot approach, I store the node positions in the long format (long) and add a frame variable to each layout. I tried to make it work with the following code, which is working fine and almost what I want. However, I cannot seem to find a way to include the edges:

ggplot(long, aes(x, y, label = name, color = as.factor(name), frame = frame)) +
  geom_point(size = 3, show.legend = F) +
  geom_text(show.legend = F) +
  transition_components(frame)

I also tried to add the edges as geom_segment but ended up with them being static while the nodes kept moving. This is why I use the ggraph package and fail:

ggraph(g, layout = "manual", node.position = long) +
  geom_node_point() +
  geom_edge_link() +
  transition_components(frame)

I'd like to have an animation of one network with changing node positions that both displays nodes and edges.

Any help is much appreciated!

Edit: I learned that one can include the layout directly into ggraph (and even manipulate the attributes). This is what I've done in the following gif. Additionally geom_edge_link0' instead of geom_edge_link is being used.

ggraph(long) +
          geom_edge_link0() +
          geom_node_point() +
          transition_states(frame)

Note that the edges are not moving.

It throws an error pointing out the difference between nodes and node positions. Which makes sense, since the network has 10 nodes and I provide 30 positions. Unfortunately, I do not know how to circumvent this. — Ben Nutzer, May 19 '19 at 16:27

Jon Spring · Accepted Answer · 2019-05-23T17:06:11.987

I'm not sure this is currently ready in gganimate as is. As of May 2019, here's what looks to be a related issue: https://github.com/thomasp85/gganimate/issues/139

EDIT I've replaced with a working solution. Fair warning, I'm a newbie with network manipulations, and I expect someone with more experience could refactor the code to be much shorter.

My general approach was to create the layouts, put the nodes into a table long2, and then create another table with all the edges. gganimate then calls the respective data source each layer needs.

1. Create the nodes table for the three layouts:

set.seed(1)
g <- erdos.renyi.game(10, .5, "gnp")
V(g)$name <- letters[1:vcount(g)]

layouts <- c("kk", "circle", "nicely")
long2 <- lapply(layouts, create_layout, graph = g) %>%
  enframe(name = "frame") %>%
  unnest()

> head(long2)
# A tibble: 6 x 7
  frame       x      y name  ggraph.orig_index circular ggraph.index
  <int>   <dbl>  <dbl> <fct>             <int> <lgl>           <int>
1     1 -1.07    0.363 a                     1 FALSE               1
2     1  1.06    0.160 b                     2 FALSE               2
3     1 -1.69   -0.310 c                     3 FALSE               3
4     1 -0.481   0.135 d                     4 FALSE               4
5     1 -0.0603 -0.496 e                     5 FALSE               5
6     1  0.0373  1.02  f                     6 FALSE               6

2. Convert the edges from the original layout into a table.

Here, I extract the edges from g and reshape into format that geom_segment can use, with columns for x, y, xend, and yend. This is ripe for refactoring, but it works.

edges_df <- igraph::as_data_frame(g, "edges") %>% 
  tibble::rowid_to_column() %>%
  gather(end, name, -rowid) %>%
  # Here we get the coordinates for each node from `long2`.
  left_join(long2 %>% select(frame, name, x, y)) %>%
  gather(coord, val, x:y) %>%
  # create xend and yend when at the "to" end, for geom_segment use later
  mutate(col = paste0(coord, if_else(end == "to", "end", ""))) %>%
  select(frame, rowid, col, val) %>%
  arrange(frame, rowid) %>%
  spread(col, val) %>%
  # Get the node names for the coordinates we're using, so that we
  #   can name the edge from a to b as "a_b" and gganimate can tween
  #   correctly between frames. 
  left_join(long2 %>% select(frame, x, y, start_name = name)) %>%
  left_join(long2 %>% select(frame, xend = x, yend = y, end_name = name)) %>%
  unite(edge_name, c("start_name", "end_name"))

> head(edges_df)
  frame rowid          x        xend          y       yend edge_name
1     1     1 -1.0709480 -1.69252646  0.3630563 -0.3095612       a_c
2     1     2 -1.0709480 -0.48086213  0.3630563  0.1353664       a_d
3     1     3 -1.6925265 -0.48086213 -0.3095612  0.1353664       c_d
4     1     4 -1.0709480 -0.06032354  0.3630563 -0.4957609       a_e
5     1     5  1.0571895 -0.06032354  0.1596417 -0.4957609       b_e
6     1     6 -0.4808621 -0.06032354  0.1353664 -0.4957609       d_e

3. Plot!

ggplot() +
  geom_segment(data = edges_df, 
               aes(x = x, xend = xend, y = y, yend = yend, color = edge_name)) +
  geom_point(data = long2, aes(x, y, color = name), size = 4) +
  geom_text(data = long2, aes(x, y, label = name)) +
  guides(color = F) +
  ease_aes("quadratic-in-out") +
  transition_states(frame, state_length = 0.5) -> a

animate(a, nframes = 400, fps = 30, width = 700, height = 300)

Thanks, this already looks very promising! However, I cannot reproduce your second code snippet. I think, I am missing some of your edge attributes from the original `g`object. — Ben Nutzer, May 22 '19 at 07:51

Smooth transitions between different layouts of the same network in ggraph

1 Answers1

1. Create the nodes table for the three layouts:

2. Convert the edges from the original layout into a table.

3. Plot!