Adding reference lines to a bar-plot with ggplot in R

Question

This is a minimal example that shows the plots I am trying to make.

Data looks like this:

plot1 = data.frame(
    Factor1 = as.factor(rep('A', 4)),
    Factor2 = as.factor(rep(c('C', 'D'), 2)),
    Factor3 = as.factor(c( rep('E', 2), rep('F', 2))),
    Y = c(0.225490, 0.121958, 0.218182, 0.269789)
)

plot2 = data.frame(
    Factor1 = as.factor(rep('B', 4)),
    Factor2 = as.factor(rep(c('C', 'D'), 2)),
    Factor3 = as.factor(c( rep('E', 2), rep('F', 2))),
    Y = c(-0.058585, -0.031686, 0.013141, 0.016249)
)

While the basic code for plotting looks like this:

require(ggplot2)
require(grid)

p1 <- ggplot(data=plot1, aes(x=Factor2, y=Y, fill=factor(Factor3))) +
    ggtitle('Type: A') +
    coord_cartesian(ylim = c(-0.10, 0.30)) +
    geom_bar(position=position_dodge(.9), width=0.5, stat='identity') +
    scale_x_discrete(name='Regime',
        labels=c('C', 'D')) +
    scale_y_continuous('Activations') +
    scale_fill_brewer(palette='Dark2', name='Background:',
        breaks=c('E','F'),
        labels=c('E','F')) +
    theme(axis.text=element_text(size=11),
        axis.title.x=element_text(size=13, vjust=-0.75),
        axis.title.y=element_text(size=13, vjust=0.75),
        legend.text=element_blank(),
        legend.title=element_blank(),
        legend.position='none',
        plot.title=element_text(hjust=0.5))

p2 <- ggplot(data=plot2, aes(x=Factor2, y=Y, fill=factor(Factor3))) +
    ggtitle('Type: B') +
    coord_cartesian(ylim = c(-0.10, 0.30)) +
    geom_bar(position=position_dodge(.9), width=0.5, stat='identity') +
    scale_x_discrete(name='Regime',
        labels=c('C', 'D')) +
    scale_y_continuous('Activations') +
    scale_fill_brewer(palette='Dark2', name='Background:',
        breaks=c('E','F'),
        labels=c('E','F')) +
    theme(axis.text=element_text(size=11),
        axis.title.x=element_text(size=13, vjust=-0.75),
        axis.title.y=element_blank(),
        legend.text=element_text(size=11),
        legend.title=element_text(size=13),
        plot.title=element_text(hjust=0.5))

pushViewport(viewport(
    layout=grid.layout(1, 2, heights=unit(4, 'null'),
        widths=unit(c(1,1.17), 'null'))))
print(p1, vp=viewport(layout.pos.row=1, layout.pos.col=1))
print(p2, vp=viewport(layout.pos.row=1, layout.pos.col=2))

And the figure looks like this:

However, I would need something like this:

Thick black lines are the reference values. They are constant and the Figure presents that "reference situation". However, in other plots that I need to produce bars will change but the reference values should remain the same to make the comparisons straightforward and easy. I know I should be using geom_segment() but those lines in my attempts to make this work are just missing the bars.

Any help/advice? Thanks!

Maybe just use a geom_point for the reference; segment seems hard bc you x-axis isnt numeric. Or you could do a geom_col of the references before plotting this on top and use alpha to make it mostly see through — jeffverboon
– jeffverboon, Commented Dec 14, 2019 at 14:54

AHart · Accepted Answer · 2019-12-14 15:19:17Z

4

I was able to do this using geom_errorbarh. For instance, with the second figure:

p1 + 
  geom_errorbarh(
    aes(xmin = as.numeric(Factor2)-.2,xmax = as.numeric(Factor2)+.2), #+/-.2 for width
    position = position_dodge(0.9), size = 2, height = 0
  )

OUTPUT: And, if I understand the other plots you describe, you can specify the reference data in those, eg data = plot1

answered Dec 14, 2019 at 15:19

AHart

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Comments

dc37 · Accepted Answer · 2019-12-14 15:30:34Z

If your references are not going to be changed, you can create a second dataset and merge it to the dataset you are going to plot.

Here, I first add plot1 and plot2. Then, I create a new dataset that will be the reference dataset.

library(dplyr)
new_df = rbind(plot1, plot2)
ref_plot = new_df
ref_plot <- ref_plot %>% rename(Ref_value = Y)

Then, now you have the new_df which is the dataset to be plot and ref_plot that contains references values for each conditions.

Instead of using grid and create two different plot that I will merge after, I preferred to use facet_wrap which put all plots on the same figure. It is much more convenient and don't require to write twice the same thing.

As mentioned by @AHart few minutes before me, you can use geom_errorbar to define your reference values on the plot. The difference is I prefere to use geom_errorbar instead of geom_errobarh.

Here is for the plot:

library(ggplot2)
new_df %>% left_join(ref_plot) %>% 
  ggplot(aes(x = Factor2, y = Y, fill = Factor3))+
  geom_bar(stat = "identity", position = position_dodge())+
  geom_errorbar(aes(ymin = Ref_value-0.00001, ymax = Ref_value+0.0001, group = Factor3), position = position_dodge(.9),width = 0.2)+
  facet_wrap(.~Factor1, labeller = labeller(Factor1 = c(A = "Type A", B = "Type B"))) +
  scale_x_discrete(name='Regime',
                   labels=c('C', 'D')) +
  scale_fill_brewer(palette='Dark2', name='Background:',
                    breaks=c('E','F'),
                    labels=c('E','F')) +
  theme(axis.text=element_text(size=11),
        axis.title.x=element_text(size=13, vjust=-0.75),
        axis.title.y=element_blank(),
        legend.text=element_text(size=11),
        legend.title=element_text(size=13),
        plot.title=element_text(hjust=0.5))

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