Draw lines between all the coordinates in a plot

If you want to do this in ggplot2, then you could use geom_segment for this. But before you can make such a plot, you have to create a dataframe which connencts each observation to the other observations. You could approach it as follows:

library(ggplot2)
library(dplyr)
library(tidyr)
dat %>% 
  complete(nesting(x,y), id) %>%       # create the combinations
  select(id, xend=x, yend=y) %>%       # rename the new variables as end-points
  left_join(dat, ., by = 'id') %>%     # join with the original dataframe
  filter(!(x==xend & y==yend)) %>%     # remove the endpoints that are the same as the start points
  ggplot(., aes(x, y)) + 
  geom_segment(aes(x = x, y = y, xend = xend, yend = yend)) +
  geom_label(aes(x = x, y = y, label = id, color = factor(id)), show.legend = FALSE) +
  theme_minimal(base_size = 14) +
  theme(axis.title = element_blank())

which gives:

---

Used data:

dat <- data.frame(x = c(5,1,3,2,5,7,12), y = c(5,7,6,1,3,5,6))
dat$id <- 1:nrow(dat)

---

Alternatively, you can also add the row-id on the fly without doing it beforehand:

dat %>% 
  mutate(id = row_number()) %>%        # add a row id
  complete(nesting(x,y), id) %>%       # create the combinations
  select(id, xend=x, yend=y) %>%       # rename the new variables as end-points
  left_join(dat %>% mutate(id = row_number()), .,
            by = 'id') %>%             # join with the original dataframe (also with an added row id)
  filter(!(x==xend & y==yend)) %>%     # remove the endpoints that are the same as the start points
  ggplot(., aes(x, y)) + 
  geom_segment(aes(x = x, y = y, xend = xend, yend = yend)) +
  geom_label(aes(x = x, y = y, label = id, color = factor(id)), show.legend = FALSE) +
  theme_minimal(base_size = 14) +
  theme(axis.title = element_blank())

Using base plotting:

plot(data)
sapply(combn(nrow(data), 2L, simplify = FALSE), 
       function(x) do.call("segments", as.list(c(t(data[x, ])))))

Add bells and whistles to taste.

You may also use the FUN argument in combn:

plot(data)
combn(nrow(data), 2L, simplify = FALSE, FUN = function(cm){
  segments(x0 = data[cm[1L], 1L],
           y0 = data[cm[1L], 2L],
           x1 = data[cm[2L], 1L],
           y1 = data[cm[2L], 2L])
})