Nested facet plot with ggplot2

Question

If I have a nested factor, in this case I have multiple \"Family\" levels that are contained in the factor \"Order\", I would like to potentially create a

Answer 1

Here's a simple solution: add a variable foo to your data that collapses the levels of the inner factor such that interaction(foo, outer) has the same level sets as inner. I know I'm missing some labels, so if someone can figure out a quick way to fill in the labels I'll edit it into my answer.

library(ggplot2)
library(gridExtra)
library(dplyr)

dat <-
  structure(list(Species = c("Acanthocyclops robustus", "Acroperus harpae", 
                             "Alona affinis", "Ascaphus truei", "Bosmina longirostris"), 
                 Intercept = c(-36.1182388331068, -27.2140776216155, -25.7920464721491, 
                               -39.2233884219763, -31.4301301084581), 
                 B = c(0.919397836908493, 0.716601987210452, 0.685455190113372, 
                          1.04159758611351, 0.81077051300147), 
                 Bconf = c(0.407917065756464, 
                           0.181611850119198, 0.254101713856315, 0.708582768458448, 0.234313394549538
                          ), 
                 Order = c("Cyclopoida", "Diplostraca", "Diplostraca", "Anura", 
                           "Diplostraca"), 
                 Family = c("Cyclopidae", "Chydoridae", "Chydoridae", 
                            "Leiopelmatidae", "Bosminidae")), 
            .Names = c("Species", "Intercept", 
                       "B", "Bconf", "Order", "Family"), row.names = c(NA, 5L), class = "data.frame")

replace_with_int_rank = function (x) as.numeric(as.factor(x))
collapse_nested_factor = function( inner, outer ){
  ave(as.character(inner), outer, FUN = replace_with_int_rank )
}
dat$Family_collapsed = collapse_nested_factor(inner = dat$Family, dat$Order)
p <- ggplot(dat) + geom_point(aes(B,Species)) + facet_grid(Order~Family_collapsed, scales = "free")

Answer 2

Using facet_grid or facet_wrap will not build the graphic you are trying to build. You can, however, build a list of graphics and then plot them via gridExtra::grid.arrange. Here is an example

library(ggplot2)
library(gridExtra)
library(dplyr)

dat <-
  structure(list(Species = c("Acanthocyclops robustus", "Acroperus harpae", 
  "Alona affinis", "Ascaphus truei", "Bosmina longirostris"), Intercept = c(-36.1182388331068, 
  -27.2140776216155, -25.7920464721491, -39.2233884219763, -31.4301301084581
  ), B = c(0.919397836908493, 0.716601987210452, 0.685455190113372, 
  1.04159758611351, 0.81077051300147), Bconf = c(0.407917065756464, 
  0.181611850119198, 0.254101713856315, 0.708582768458448, 0.234313394549538
  ), Order = c("Cyclopoida", "Diplostraca", "Diplostraca", "Anura", 
  "Diplostraca"), Family = c("Cyclopidae", "Chydoridae", "Chydoridae", 
  "Leiopelmatidae", "Bosminidae")), .Names = c("Species", "Intercept", 
  "B", "Bconf", "Order", "Family"), row.names = c(NA, 5L), class = "data.frame")

dat

# A ggplot object with NO data.  Omit the order from the facet_grid call
g <- 
  ggplot() +
  aes(Species, B) +
  geom_point() +
  facet_grid(. ~ Family,
             scales = "free", space = "free") +
  ylim(range(dat$B)) +
  xlab("")

# Build a seperate graphic for each Order and title
plots <-
  lapply(unique(dat$Order), function(o) {
           g %+% dplyr::filter_(dat, ~ Order == o) + ggtitle(o)
             })

# build as Grobs and plot via gridExtra::grid.arrange
plots %>%
  lapply(ggplotGrob) %>%
  arrangeGrob(grobs = .) %>%
  grid.arrange(., ncol = 1)