A bit of code for simulating site areas and environmental gradients to be plotted as two networks in both geographic and feature space. Supporting a graphic in this tweet: https://twitter.com/Md_Harris/status/851983574249209856

ggraph_transformed_space.R

library("ggraph")
library("igraph")
library("ggplot2")

# create some simulated sites that contain various numbers of measurements on a regular grid
site_dat <- data.frame(size = rep(c("A","B","C","D"), times = c(3,4,8,5)),
                       x    = c(25,26,26,
                                40,41,41,40,
                                15,16,17,17,16,15,15,16,
                                40,41,42,42,41),
                       y    = c(28,28,29,
                                7,7,8,8,
                                10,10,10,11,11,11,12,12,
                                40,40,40,41,41),
                       stringsAsFactors = FALSE) 
# scale/center the coordinates for plotting purposes
site_dat$x_c <- as.numeric(scale(site_dat$x))
site_dat$y_c <- as.numeric(scale(site_dat$y))

# Create simulated environmental gradients for elevation and distance to water
elev <- expand.grid(x = 0:50, y  = 0:50) %>%
  data.frame() %>%
  mutate(elev = exp(-(x-40)^2 / (2*8^2)),
         elev_c = as.numeric(scale(elev)))
h20 <- expand.grid(x = 0:50, y  = 0:50) %>%
  data.frame() %>%
  mutate(h20 = (50-x)^2*(50-y)^2,
         h20_c = as.numeric(scale(h20)))
var_space <- full_join(elev, h20, by = c("x", "y"))

# join the environmental measurements to the sites
site_dat <- site_dat %>%
  left_join(var_space, by = c("x", "y"))

# create a new data.frame that gathers coords for geographic and feature space
# slighlty tortured here, but it was late when I wrote it! 
site_dat2 <- data.frame(size  = c(site_dat$size, paste0(site_dat$size, "_c")),
                        x_c   = c(site_dat$x_c, site_dat$elev_c),
                        y_c   = c(site_dat$y_c, site_dat$h20_c),
                        model = rep(c("geographic space", "feature space"), each = nrow(site_dat)))
# a data.frame of the network connections... I know 'df2' is a terrible name.
df2 <- data.frame(from = c(rep(c("A","B","C","D"), each = 4),
                           rep(c("A_c","B_c","C_c","D_c"), each = 4)),
                  to    = c(rep(c("A","B","C","D"), times = 4),
                            rep(c("A_c","B_c","C_c","D_c"), times = 4)),
                  stringsAsFactors = FALSE)
# grab the coordinates (in both spaces) for the points
meta2 <- group_by(site_dat2, size) %>%
  summarise(x = mean(x_c), y = mean(y_c)) %>%
  mutate(label = substr(size,1,1))
# use igraph functions to grab a unique edge list
df2 <- unique(get.data.frame(graph.data.frame(df2, directed=FALSE, 
                                              vertices = meta2),"edges"))
# run the graph on the unique edges with coordinates as vertices.
g2 <- graph.data.frame(df2, directed = FALSE, vertices = meta2)

# plot with ggraph package
ggraph(g2, layout = 'manual', node.positions = meta2) + 
  # plot edges with different colors 
  geom_edge_hive(aes(alpha = ..index.., color = rep(c("red", "blue"), each = 10)),
                 show.legend = FALSE) + 
  # plot the points for both sets of data
  geom_point(data = site_dat2,  aes(x_c, y_c, color = factor(model)), size = 2) +
  # plot labels
  geom_text(data = meta2,  aes(x, y, label = label), size = 4,
            nudge_x = 0.15, nudge_y = 0.15, family = "Trebuchet MS") +
  # theme
  theme_minimal() +
  coord_fixed() +
  # set scales
  scale_x_continuous(breaks = seq(-1, 2, by = 0.5), labels = seq(-1, 2, by = 0.5)) +
  scale_y_continuous(breaks = seq(-1, 2, by = 0.5), labels = seq(-1, 2, by = 0.5)) +
  # Labels
  labs(x = "X/Elevation",
       y = "Y/H2O",
       title = "Coordinate Space Transformation",
       subtitle = "") +
  # this hack removes the title of the legend
  scale_color_discrete("") +
  # theme elements for making it pretty
  # If you do not have 'Trebuchet' font, you may want to remove those calls to 'family=...'
  theme(
    plot.title=element_text(family="TrebuchetMS-Bold", size = 11, hjust = 0.35),
    legend.position = "bottom",
    legend.text = element_text(family = "Trebuchet MS", size = 9),
    panel.grid.major = element_blank(), 
    panel.grid.minor = element_blank(),
    axis.text.x = element_text(angle = 90, hjust = 1, 
                               size = 8, family = "Trebuchet MS"),
    axis.text.y = element_text(size = 8, family = "Trebuchet MS"),
    axis.title = element_text(size = 8, family = "Trebuchet MS", face = "bold")
  )

ggsave("coord_transform.png", width = 4, height = 6)