Fine tuning ggplot2's geom boxplot

Question

I have this data.frame

my.df = data.frame(mean = c(0.045729661,0.030416531,0.043202944,0.025600973,0.040526913,0.046167044,0.029352414,0.021477789,0.02758052         


        

Answer 1

You can use geom_segment to add center lines. I use an alpha parameter for the start and end of the line centered in replicate.

library(ggplot2)
alpha=0.3

p1 = ggplot(data = my.df, aes(factor(replicate), 
                              color = factor(parent.origin)))
p1 = p1 + geom_boxplot(aes(fill = factor(parent.origin), 
                           lower = mean - std.dev, 
                           upper = mean + std.dev, 
                           middle = mean, 
                           ymin = mean - 3*std.dev, 
                           ymax = mean + 3*std.dev), 
                       width = 0.3, 
                       linetype="dotted",
                       stat="identity") + 
  facet_wrap(~group, ncol = 4)+ 
  scale_color_manual(values = c("red","blue"),labels = c("maternal","paternal"),
                     name = "parental allele")+
  scale_fill_manual(values = c("red","blue")) +
  geom_segment(aes(x = replicate-alpha, 
                   y = mean, 
                   xend = replicate+alpha, 
                   yend = mean),
               inherit.aes=FALSE,color="black",size=1.5)


p1

Answer 2

Here's what worked for me:

p1 = ggplot(data = my.df, aes(factor(replicate), color = factor(parent.origin)))
p1 = p1 + geom_boxplot(aes(fill = factor(parent.origin),lower = mean - std.dev, 
     upper = mean + std.dev, middle = mean, ymin = mean - 3*std.dev, 
     ymax = mean + 3*std.dev), position = position_dodge(width = 0), width = 0.5, 
         alpha = 0.5, stat="identity") + 
     facet_wrap(~group, ncol = 4)+
     scale_fill_manual(values = c("red","blue"),labels = c("maternal","paternal"),
         name = "parental allele")+
     scale_colour_manual(values = c("red","blue"),labels = c("maternal","paternal"),
         name = "parental allele")

The width value within the position_dodge parameter determines the separation between the red and blue boxes per each replicate, and the other width parameter controls the width o he box. The alpha value controls transparency.