ggplot barchart with grouped confidence interval

Question

enter image description here

a <- structure(list(
  X1 = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L), 
                  .Label = c("V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8"), class = "factor"), 
   X2 = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,  2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), 
                    .Label = c("A", "B", "C"), class = "factor"), 
  value = c(0.03508924, 0.03054929, 0.03820896, 0.18207091, 0.25985142, 0.03909991, 0.03079736, 
            0.41436334, 0.02957787, 0.03113289, 0.03239794, 0.1691519, 0.16368845, 0.0287741, 0.02443448, 
            0.33474091, 0.03283068, 0.02668754, 0.03597605, 0.17098721, 0.23048966, 0.0385765, 0.02597068, 0.36917749), 
   se = c(0.003064016, 0.003189752, 0.003301929, 0.006415592, 0.00825635, 0.003479607, 
          0.003195332, 0.008754099, 0.005594554, 0.006840959, 0.006098068, 0.012790908, 0.014176414, 
          0.006249045, 0.005659445, 0.018284739, 0.005051873, 0.004719352, 0.005487301, 0.011454206, 
          0.01290797, 0.005884275, 0.004738851, 0.014075813)), 
  .Names = c("X1", "X2", "value", "se"), class = "data.frame", row.names = c(NA, -24L))

I'm plotting the above data (kept in dataset "a"), and I can't get the confidence interals to sit in the middle of the group chart.My attempts until now have only managed to put lines on the side of each bar, not in the middle like in the geom_errorbar helpfile.I've tried to manipulate the dodge parameters but it only made it worse. The chart needs to stay flipped over and in the code below I used geom_linerange but geom_errorbar would be even better. Another thing I haven't quite managed to do is to change the scale into whole numbers (without muliplying the original table ).

I've used the code below on a<-a[1:16,] (the first two groups). When I use the same code on the full table I get even worse results with the confidence intervals. Would anyone be able to help? Many thanks in advance.

limits <- aes(ymax = value + se, ymin=value - se)
 p<-ggplot(data = a, aes(x = X1, y =value))+   
    geom_bar(aes(fill=X2),position = "dodge") +    
    scale_x_discrete(name="")+
    scale_fill_manual(values=c("grey80","black","red"))+
    scale_y_continuous(name="%")+   
    theme(axis.text.y = element_text(face='bold'),
          legend.position ="top",
          legend.title=element_blank())+   
     coord_flip()
p + geom_linerange(limits)

you miss to include limits? If I understand you want to add a line on each bar? — agstudy, Nov 29 '12 at 15:13

agstudy · Accepted Answer · 2012-11-29T16:27:02.883

2

Try this ,

p<-ggplot(data = df, aes(x = X1, y =value,fill= X2))+   
    geom_bar(position=position_dodge()) +
    geom_errorbar(aes(ymax = value + 2* se, ymin=value,colour = X2),position=position_dodge(.9))



p <- p + scale_x_discrete(name="")+
   scale_fill_manual(values=c("grey80","black","red"))+
   scale_y_continuous(name="%")+   
   theme(axis.text.y = element_text(face='bold'),
         legend.position ="top",
         legend.title=element_blank())+   
   coord_flip()

enter image description here

edited Nov 29 '12 at 16:27

answered Nov 29 '12 at 15:34

agstudy

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Agstudy,I'm really sorry.I posted this too quickly. In my attempt to anonymise the data I actually mislabeled the variables! I've amended the dataset now and re-run the code. You should be able to see what my problem is now. I'm really sorry if I've wasted your time. – maycobra Nov 29 '12 at 15:57
to give a reproducible sample of your data, use dput , type dput(a) and amnend your question. – agstudy Nov 29 '12 at 16:02
Thank you very much. And scale_y_continuous(name="%",labels=function(x)x*100) should amend the scale as I mentioned (see http://stackoverflow.com/questions/4646020/ggplot2-axis-transformation-by-constant-factor) – maycobra Nov 29 '12 at 17:03

ggplot barchart with grouped confidence interval

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