I would like to create a plot using ggplot where different facets should have different y axis limits. By default each facet has the same y axis values. can this be changed
You can change scales to "free_y" instead.
scales
facet_grid(facets, margins = FALSE, scales = "fixed", space = "fixed", shrink = TRUE, labeller = "label_value", as.table = TRUE, drop = TRUE)
For further detail and examples, see: http://docs.ggplot2.org/0.9.3.1/facet_grid.html