Question

In ggplot2 I’m attempting a simple thing that I just can’t get for some reason. I have adjusted means and SE in a data frame and want to plot the means, error bars and then connect the means with points. Here’s the code and the error (it does everything except connect the means with geom_line (working with RCookbook:

library(ggplot2)
#data set
data1 <- structure(list(group = structure(1:3, .Label = c("1", "2", "3"
), class = "factor"), estimate = c(55.7466654122763, 65.0480954172939, 
61.9552391704298), SE = c(2.33944612149257, 2.33243565412438, 
2.33754952927041), t.ratio = c(23.8290016171476, 27.8884844271143, 
26.5043535525714)), .Names = c("group", "estimate", "SE", "t.ratio"
), row.names = c(NA, 3L), class = "data.frame")

#the attempted plot
pd <- position_dodge(.1)
ggplot(data1, aes(x=group, y=estimate, group=group)) + 
    geom_errorbar(aes(ymin=estimate-SE, ymax=estimate+SE), 
        colour="black", width=.1, position=pd) +
    geom_line(data=data1, aes(x=group, y=estimate)) + 
    geom_point(position=pd, size=4)

the error:

ymax not defined: adjusting position using y instead
geom_path: Each group consist of only one observation. Do you need to adjust the group aesthetic?

Answer 1

If you remove the grouping by group within the ggplot call and set x = as.numeric(group ) within the call to geom_line, the it works.

Also, you don’t need to re-reference data1 within geom_line

ggplot(data1, aes(x=group, y=estimate)) + 
  geom_errorbar(aes(ymin=estimate-SE, ymax=estimate+SE), 
  colour="black", width=.1, position=pd) +
  geom_line( aes(x=as.numeric(group), y=estimate)) + 
  geom_point(position=pd, size=4)

If you group by group, then you only have one value for geom_line to create a line from, hence the error message. The same error occurs if ggplot is considering the x or y mapping variables as a factor – this is because if you code a variable as a factor R (and ggplot) will consider them independent groups, and not connect the points – this is sensible default behaiviour.

EDIT – with alphabetic factor labels

This will work with alphabetic factor labels due to the way factors are coded internally by R (ie as.numeric(factor) returns numbers not the factor labels)

ie.e

Changing group to a, b, c

levels(data1[['group']]) <- letters[1:3] 
ggplot(data1, aes(x=group, y=estimate)) + 
  geom_errorbar(aes(ymin=estimate-SE, ymax=estimate+SE), 
  colour="black", width=.1, position=pd) +
  geom_line( aes(x=as.numeric(group), y=estimate)) + 
  geom_point(position=pd, size=4)