Gene Ontology Bubble Plot using ggplot2

So with your data that seems to look something like this:

structure(list(GO_term = structure(c(2L, 4L, 3L, 1L), .Label = c("Kinase", 
"Metabolism", "Nucleus", "Photosynthesis"), class = "factor"), 
    Number = c(5L, 10L, 15L, 16L), Class = structure(c(3L, 2L, 
    1L, 1L), .Label = c("hs", "hzs", "start_duf"), class = "factor"), 
    Type = structure(c(1L, 1L, 2L, 3L), .Label = c("BP", "CC", 
    "MF"), class = "factor")), class = "data.frame", row.names = c(NA, 
-4L))

You could work with geom_tile and set its width = Inf to get something akin to that plot you’re trying to emulate. The use of forcats::reorder() within aes() is important in order to group the Y-axis values together on the basis of your Type column.

library(ggplot2)
library(forcats)

ggplot(mydat, aes(y = reorder(GO_term, as.numeric(Type)), x = Number, size = Number)) + geom_point(aes(color = Class), alpha = 1.0) + 
  geom_tile(aes(width = Inf, fill = Type), alpha = 0.4) + 
  scale_fill_manual(values = c("green", "red", "blue"))

Which yields:

The problem you’d probably run into is having to pass the appropriate number of colors to scale_fill_manual for your actual dataset.