Question

Using this data:

library(ggplot2)
dd <- data.frame(id = c("A", "A", "B", "B"), prepost = c("pre", "post"), 
         value = 1:4)

this one works:

qplot(id, value, data = dd, fill = prepost, geom = "bar")

however, the next one gives the indicated error message. The only difference between the two is the addition of group = prepost to the end of the command; however, since we had already written fill = prepost that should be the default group anyways.

> qplot(id, value, data = dd, fill = prepost, geom = "bar", group = prepost)
 Error in pmin(y, 0) : object 'y' not found

We can fix up the last one by adding stat = "identity" like this:

qplot(id, value, data = dd, fill = prepost, geom = "bar", group = prepost, 
      stat = "identity")

I have two questions:

(a) Why does the qplot which gave the error message not work when the others do work?

(b) If we use a continuous y aesthetic with geom_bar then what is supposed to happen if one does not specify stat? From the first qplot it seems that in that case it acts as if stat="identity" but in the presence of group specifying stat="identity" or not reveals a difference.

(By the way, this question seems somewhat related although its different enough that it does not seem to answer this question: Issue with ggplot2, geom_bar, and position="dodge": stacked has correct y values, dodged does not)

Answer 1

A good question!

I will echo a earlier comment by @joran

I generally find that people are less confused with ggplot once they learn to stop using qplot

Your qplot call can be recreated using

ggplot(dd) + geom_bar(aes(x = id, y = value, fill = prepost))

Now, if you read the help for geom_bar it lists the aesthetics it understands, group is not one of them (so perhaps you can’t expect it to work as you wish when you do this)

If you read the help for group you will see that it is an aesthetic that allows you to override the default interaction of all discrete variables.

If you group by prepost alone, you are not grouping by the discrete x axis variable id, which the default would be included as well,

Therefore

ggplot(dd) + 
 geom_bar(aes(x=id, y = value, fill = prepost, group = interaction(id, prepost)))

works, but the grouping is entirely redundant as this is the default.

If you specify just prepost or id as your grouping, it confuses stat_bin (the underlying method that is crunching the numbers to create the values for the bar plot. Hence you need to use stat_identity instead.

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EDIT: as noted by the OP in the comments below, this is related to a known issue and will give better warnings in the next version (or th current dev version on github

From the NEWS

• stat_bin now produces warning messages when it is used with set or
  mapped y values. Previously, it was possible to use stat_bin and
  also set/map y values; if there was one y value per group, it would
  display the y values from the data, instead of the counts of cases for
  each group. This usage is deprecated and will be removed in a future
  version of ggplot2. (Winston Chang. Fixes #632)