How to add inbetween space in nested boxplots ggplot2

Question

I would like to added a marginal space between groups of box plots by using the stats_summary method.

Here is a small example of my problem

library(ggplot2)
library(reshape2)
data1 <- (lapply(letters[1:5], function(l1) return(matrix(rt(5*3, 1), nrow = 5, ncol = 3, dimnames = list(cat2=letters[6:10], cat3=letters[11:13])))))
names(data1) <- letters[1:5]
data2 <- melt(data1)

customstats <- function(x) {
  xs <- sort(x)
  return(c(ymin=min(x), lower= mean(xs[xs < mean(x)]), middle = mean(x) , upper = mean(xs[xs > mean(x)]), ymax=max(x)))
}

ggplot(data2, aes(x=cat2, y=value, fill=cat3), width=2) + 
  stat_summary(fun.data = customstats, geom = "boxplot", 
    alpha = 0.5, position = position_dodge(1), mapping = aes(fill=cat3))

The result is the following picture. boxplots

I would like to achieve a visual separation for each "cat2" and add a "space" between the group of boxplots (I'm retricted to using the stats_summary since I have a custom statistic). How can I do it?

Probably the safest bet is to use geom_bar on manually precomputed data. Actually, this is the only possible method I see. — tonytonov
– tonytonov, Commented Jun 17, 2015 at 12:13
not ideal but you could use facets: + facet_grid(.~cat2, scales = "free_x") — user20650
– user20650, Commented Jun 17, 2015 at 12:29
That would work on one graph, yes. In my particular case (not in the example) I already have a facet_grid based on additional variables and thus cannot use your solution. — Drey
– Drey, Commented Jun 17, 2015 at 12:39

user20650 · Accepted Answer · 2015-06-17 15:54:46Z

4

I have fixed a similar problem in an ugly (but effective for me) way by creating a dataframe with the same plotting variables as my original data, but with x (or y) positioned or factored that it fits between the two points I want to separate and missing values for y (or x). For your problem, I added the following code and got an image with spacial separation of clusters.

library(plyr)

empties <- data.frame(cat2_orig=unique(data2$cat2)[-length(unique(data2$cat2))])
#no extra space needed between last cluster and edge of plot
empties$cat2 <- paste0(empties$cat2_orig,empties$cat2_orig)
empties$value <- NA


data2_space <- rbind.fill(data2,empties)

ggplot(data2_space, aes(x=cat2, y=value, fill=cat3), width=2) + 
  stat_summary(fun.data = customstats, geom = "boxplot", 
           alpha = 0.5, position = position_dodge(1), mapping =     aes(fill=cat3)) +
#remove tickmarks for non-interesting points on x-axis
  scale_x_discrete(breaks=unique(data2$cat2))

Before & after

enter image description here

edited Jun 17, 2015 at 15:54

user20650

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answered Jun 17, 2015 at 14:21

Heroka

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4 Comments

Drey Over a year ago

Thanks, it seems to work, but i don't get why. Unfortunately does not work for my actual data, but i will try to adapt the technique.

Heroka Over a year ago

You're welcome! It works because it creates extra factor levels and plots them (but there's nothing to plot --> empty space). The scale_x_discrete then only adds ticks and labels to the original factor levels. If you have an example of your actual data, I'm willing to have a look at it to adapt it.

Drey Over a year ago

Thanks again. The problem i got is that the plot consists of faceset and that it showed the NA x NA empty facets. The solution was to expand.grid(unique(facet1), unique(facet2), additional_empty_factors) and then to rbind them to the data_space. That worked.

Heroka Over a year ago

Good to know! Are you happy with the spacing? I also have tricks for that, but it gets even uglier.

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