Question

I want to set my outlier points in a boxplot to be semitransparent
In here! they used “jitter” (similar idea, different approach)

my code

ggplot() + 
geom_boxplot(aes(x = Sistema, y=values, linetype = Sistema), 
             data=estacado, outlier.size=1, outlier.shape=2) + 
coord_flip() + 
labs(x="Sistema", y=expression(paste("RMSD ",(ring(A))))) +
opts(legend.position="none")

my data

>head(estacado)
    values   ind Sistema
1 0.310214 r24_a     R24
2 0.428232 r24_a     R24
3 0.460971 r24_a     R24
4 0.482923 r24_a     R24
5 0.492656 r24_a     R24
6 0.515591 r24_a     R24
> tail(estacado)
          values   ind Sistema
4999995 1.723030 g24_e     G24
4999996 1.718444 g24_e     G24
4999997 1.720745 g24_e     G24
4999998 1.737137 g24_e     G24
4999999 1.733106 g24_e     G24
5000000 1.738487 g24_e     G24

http://dl.dropbox.com/u/19202810/Rplot01.png http://dl.dropbox.com/u/19202810/Rplot01.png

In the mentioned link, they modified the function geom_boxplot; I was hoping something more easy like outlier.colour= alpha("black", 1/2) but that gives the error:

Error in do.call("layer", list(mapping = mapping, data = data, stat = stat,  : 
  could not find function "alpha"

Any help is appreciated.

Answer 1

As of ggplot2 version 0.9.0, the alpha function was moved to the (then new) scales package. To use it, you need to include

library("scales")

in addition to

library("ggplot2")

in your script.