Add second facet grid or second discrete y-axis

[ahamel16]

Hi all,

Suppose I have this dataframe:

df2 <- data.frame(tissue = c("Blood", "Nerve", "Stomach", "Liver", "Blood", "Kidney"),
                  qtl = c("e", "s", "e", "e", "s", "s"),
                  gene = c("gene1", "gene1", 
                           "gene2", "gene2",
                           "gene3", "gene4"),
                  value = c(0.4, 0.2, 0.1, 0.9, 0.5, 0.3),
                  second_label = c("label1", "label1", "label1","label1",
                                  "label2", "label2"))

And plot it as such:

ggplot(df2, 
       aes(x=tissue, y=qtl,
           size=value))+
  geom_point()+
  facet_grid(rows = vars(gene),
             scales = "free", 
             space='free',
             switch = "y")+
  theme(axis.title.x = element_blank(),
        axis.text.x = element_text(size=8,angle = 90, hjust=1, vjust=0.2),
        axis.title.y = element_blank(),
        axis.text.y = element_text(size=8),
        axis.ticks.y = element_blank(),
        axis.line = element_line(color = "black"),
        strip.text.y.left = element_text(size = 8, angle=0),
        strip.background = element_blank(),
        panel.spacing.y = unit(0.5, "lines"),
        strip.placement = "outside",
        panel.background = element_blank(),
        panel.grid.major = element_line(colour = "#ededed", size = 0.5))
  

This yields the following plot:

However, what if I wanted to add a second facet grid label or second y-axis being the loci column. I've seen that you can do a facet_grid on two variables where one is the column and one is the row. How do I get it so that they are both rows?

I've looked into having it as a second y-axis but that seems to only work for continuous variables.

The desired plot I'm looking for is this:

Thanks in advance!

[Axeman]

I think the best you can do (easily) is this:

Using only ggplot2:

ggplot(df2, aes(x = tissue, y = qtl, size = value)) +
  geom_point() +
  facet_grid(
    rows = vars(second_label, gene),
    scales = "free", 
    space = 'free',
    switch = "y"
  ) +
  your_theme

Or with an extension package:

library(ggh4x)
ggplot(df2, aes(x = tissue, y = qtl, size = value)) +
  geom_point() +
  facet_nested(
    rows = vars(second_label, gene),
    scales = "free", 
    space = 'free',
    switch = "y"
  ) +
  your_theme

[ahamel16]

Thank you! This is very helpful. Is there any way to move the second_label to the right side and keep the gene facet on the left? Or do they both have to be on the same side?

[Axeman]

Not easily (i.e without hacking ggplot internals), at least that I know of.

Or I suppose you could draw the text manually using annotate or similar (also cumbersome).

[ahamel16]

Good to know. I tried to do it manually on the right side using the secondary y-axis, but it has to be continuous so it did not work.

[ahamel16]

One last question:

Is there a simple way to right (or left) justify the gene facet labels? It seems the issue is non-trivial.

[Axeman]

It helps if you show what you have tried.

I think you can only change the justification of all facet labels (strip text) at the same time. E.g.

theme(strip.text = element_text(size = 8, angle = 0, hjust = 0))