Changing whisker definition in geom_boxplot

Question

I'm trying to use ggplot2 / geom_boxplot to produce a boxplot where the whiskers are defined as the 5 and 95th percentile instead of 0.25 - 1.5 IQR / 0.75 + IQR and outliers from those new whiskers are plotted as usual. I can see that the geom_boxplot aesthetics include ymax / ymin, but it's not clear to me how I put values in here. It seems like:

stat_quantile(quantiles = c(0.05, 0.25, 0.5, 0.75, 0.95)) 

should be able to help, but I don't know how to relate the results of this stat to set the appropriate geom_boxplot() aesthetics:

geom_boxplot(aes(ymin, lower, middle, upper, ymax)) 

I've seen other posts where people mention essentially building a boxplot-like object manually, but I'd rather keep the whole boxplot gestalt intact, just revising the meaning of two of the variables being drawn.

Answer 1

geom_boxplot with stat_summary can do it:

# define the summary function f <- function(x) {   r <- quantile(x, probs = c(0.05, 0.25, 0.5, 0.75, 0.95))   names(r) <- c("ymin", "lower", "middle", "upper", "ymax")   r }  # sample data d <- data.frame(x=gl(2,50), y=rnorm(100))  # do it ggplot(d, aes(x, y)) + stat_summary(fun.data = f, geom="boxplot")  # example with outliers # define outlier as you want     o <- function(x) {   subset(x, x < quantile(x)[2] | quantile(x)[4] < x) }  # do it ggplot(d, aes(x, y)) +    stat_summary(fun.data=f, geom="boxplot") +    stat_summary(fun.y = o, geom="point") 

Answer 2

It is now possible to specify the whiskers endpoints in ggplot2_2.1.0. Copying from the examples in ?geom_boxplot:

 # It's possible to draw a boxplot with your own computations if you  # use stat = "identity":  y <- rnorm(100)  df <- data.frame(    x = 1,    y0 = min(y),    y25 = quantile(y, 0.25),    y50 = median(y),    y75 = quantile(y, 0.75),    y100 = max(y)  )  ggplot(df, aes(x)) +    geom_boxplot(     aes(ymin = y0, lower = y25, middle = y50, upper = y75, ymax = y100),     stat = "identity"   )