How to add vertical lines to ggplot boxplots in R

Question

I am plotting boxplots from this data:

MY_LABEL     MY_REAL     MY_CATEGORY
1 [POS]       .56            POS
1 [POS]       .57            POS
1 [POS]       .37            POS
2 [POS]       .51            POS
1 [sim v]     .65            sim v
...

I'm using ggplot2:

ggplot( data=myDF, aes( x=MY_LABEL, y=MY_REAL, fill=MY_CATEGORY ) ) +
    scale_colour_manual( values=palette ) +
    coord_flip() + 
    geom_boxplot( outlier.size = 0 )

This works fine, and groups the boxplots by the field MY_CATEGORY:

I'd like to do 2 things:

1) To improve the clarity of this plot, I'd like to add separators between the various blocks, i.e. between POS and sim v, between sim v and C, etc (see the ugly red lines in the plot). I've been struggling with geom_vline with no luck. Alternatively, I'd like to add blank space between the blocks.

2) If I print this plot in grayscale, I can't distinguish the different blocks. I'm trying to force a different palette with:

scale_colour_manual( values=c("black","darkgray","gray","white") )

Again, no luck, the plot doesn't change at all.

What would you suggest to do?

Answer 1

Would this work for you?

require(ggplot2)
mtcars$cyl2<- ifelse(mtcars$cyl > 4, c('A'), c('B')) 
p <- ggplot(mtcars, aes(factor(cyl), mpg))
p + geom_boxplot() + facet_grid(. ~ cyl2, scales = "free", space = "free")

would give something like this,

Answer 2

To change the fill colors, you need a named vector of values. The names need exactly match the y-axis category names.

scale_fill_manual(values=c("POS"="black", "sim v"="gray50",
                           "C"="gray80", "sim t"="white"))

To separate the y-axis categories, try facet_grid().

facet_grid(factor(MY_CATEGORY) ~ ., drop=TRUE)

I'm not sure that this will work because I don't have your data to test it.

Answer 3

No one covered the horizontal line route, so I thought I'd add it. Not sure why geom_vline() wasn't working for you. Here's what I did (chose to play off of Eric Fail's approach):

require(ggplot2)
p <- ggplot(mtcars, aes(factor(cyl), mpg))
p <- p + geom_boxplot(aes(fill=factor(cyl))) + coord_flip()
p <- p + geom_vline(xintercept=c(1.5,2.5))
p

There's only three boxplots here, but in playing around, ggplot appears to place them at integer locations. Just figure out which box you want a line after (nth) and put the xintercept argument at n+0.5 for the line. You can obviously change the thickness and color to your liking: just add a size=width and colour="name" after the xintercept bit.

By the way, geom_vline() seems to work for me regardless of whether it's before or after coord_flip(). I find that counter-intuitive.

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I'm not sure bdemarest is correct that you need the names to match the category names. I think the issue is that you used scale_colour_manual(), which applies if you used aes(..., colour=var) whereas you used fill=var. Thus, you need scale_fill_manual. Building on the above, we can add:

p <- p + scale_fill_manual(values=c("black","gray","white"))
p

Note that I've not defined any factor names for the colors to match. I think the colors are simply applied to your factor levels according to their order, but I could be wrong.

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The end result of all of the above: