ggplot2- geom_linerange with stat_smooth

Question

Oh wise ones: I've got a question about the use of geom_linerange(), attached is what I hope is a workable example to illustrate my problem.

b=c(100,110,90,100,120,130,170,150,150,120,140,150,120,90,90,100,40,50,40,40,20,60,30)
test<-data.frame(a=c(2,2,2,4,4,4,4,6,6,6,6,6,6,8,8,8,10,10,10,10,10,10,10),
                 b=b,c=c(b-15))

testMelt <- melt(
  test, 
  id       = c("a"), 
  measured = c("b", "c")
  )


p <- ggplot(
  aes(
    x    = factor(a), 
    y    = value,
    fill= variable
    ),      
   data  = testMelt) + 
    geom_boxplot() + 
          stat_smooth(aes(group=variable,x=factor(a),y=value,fill=factor(variable)),data=testMelt)

My actual dataset is much larger, and the boxplots are a bit overwhelming. I think what I want is to use geom_linerange() somehow to show the range of the data, at "b" and "c", at each value of "a".

The best I've come up with is:

p<- p+ geom_linerange(aes(as.factor(a),ymin=min(value),ymax=value,color=variable))

I can assume the "c" values are always equal to or less than "b", but if the range is smaller, this "covers it up". Can I jitter the lines somehow? Is there a better solution?

Answer 1

In your geom_linerange call, add an additional argument position=position_dodge(width=0.3) . You can adjust the absolute width to change the separation between the vertical lines.

Answer 2

My understanding of the question is that you want the line range to reflect the range for the combination a:b:c .

geom_linerange(aes(as.factor(a),ymin=min(value),ymax=value,color=variable)) will set the minimum value to the whole-dataset minimum (hence all the lines appear with the same minimum value.

A couple of solutions.

Calculate the minima and maxima yourself

test_range <- ddply(testMelt, .(a,variable), summarize, 
                    val_min = min(value), val_max = max(value))

then run

 ggplot(data  = testMelt) + 
    geom_boxplot(aes(x = factor(a), y = value, fill = variable)) + 
    stat_smooth(aes(group = variable, x = factor(a), y = value, 
                    fill = factor(variable))) +
     geom_linerange(data = test_range, aes(x = as.factor(a), ymin = val_min,
                    ymax = val_max, color = variable), 
                    position = position_dodge(width = 0.3))

Or, for an alternative to boxplots / line range use a violin plot.

ggplot(data  = testMelt) + 
    geom_violin(aes(x = factor(a), y = value, fill = variable)) + 
    stat_smooth(aes(group = variable, x = factor(a), y = value, 
                    fill = factor(variable)))