How do I change the shape of the legend key glyph to a hexagon in ggplot2?

You can create keys using grid commands and then pass to a geom_ using the key_glyph argument.

A quick example:

library(grid)
library(ggplot2)

draw_key_hex <- function (data, params, size) {
    # hexagon vertex coordinates 
    v <- list(x = c(0.95, 0.725, 0.275, 0.05, 0.275, 0.725), 
              y = c(0.5, 0.110288568297003, 0.110288568297003, 0.5, 0.889711431702997, 0.889711431702997))
    # hexagon grob
    polygonGrob(v$x, v$y, 
                gp = gpar(col = data$colour,
                          fill = alpha(data$fill, data$alpha)))
}

set.seed(123)
ggplot(iris, aes(x=Species,y=Sepal.Length,color=Species)) +
  geom_jitter(width=0.25, key_glyph=draw_key_hex) 

# or with fill
set.seed(123)
ggplot(iris, aes(x=Species,y=Sepal.Length,color=Species, fill=Species)) +
  geom_jitter(width=0.25, key_glyph=draw_key_hex)