How to get different colors related to treatment for boxplot and violin plot (ggplot / using geom_split_violin) that are plotted in one?

Question

I am trying to show a boxplot and a violin plot in one.

I can fill in the colors of the boxplot and violin plot based on the treatment. But, I don't want them in exactly the same color, I'd prefer the violin plot or the boxplot filling to be lighter.

Also, I am able to get the outer lines of the boxplot in different colors if I add col=TM to the aes of the geom_boxplot. But, then I can not choose these colors or don't know how to (they are now automatically pink and blue).

BACKGROUND:

I am working with a data set that looks something like this:

TM        yax    X       Zscore
Org   zscore  zhfa    -1.72
Org   zscore  zfwa    -0.12

I am plotting the z-scores based on the X (zhfa e.d.) per treatment (TM).

#Colours
ocean = c('#BBDED6' , '#61C0BF' , '#FAE3D9' , '#FFB6B9' )

## Plot ##
z <- ggplot(data = data, aes(x = X, y = Zscore,fill=TM)) +
      geom_split_violin(col="white", fill="white")  +
      geom_boxplot(alpha = 1, width=0.3, aes(fill=TM), position = position_dodge(width = 0.3))          

z + theme(axis.text = element_text(size = 12),legend.position="top")  +
    stat_compare_means(method="t.test", label.y=2.8, label.x=0.3, size=3) +
    scale_fill_manual(values=ocean, labels=c("Mineral fertilizer", "Organic fertilizer"))

Now, half of the violin plot is filled white, but not both (which would already be better). If I would plot geom_split_violin() it would get exactly the same colors as the boxplot.

Furthermore, should the violinplot of zhfa be on the left side but it get's switched and is displayed at the right side, while it matched the data of the organic (left) boxplot.

The graph now:

I don't know if it can be solved by adding something related to the scale_fill_manual or if this is an impossible request

Sample Data:

data <- data.frame(TM = c(rep("org", 5), rep("min", 5),rep("org", 5), rep("min", 5),rep("org", 5), rep("min", 5)),
                 Zscore = runif(30,-2,2),
                 X = c(rep("zwfa", 10), rep("zhfa", 10), rep("zbfa", 10)))

Could you add data to your question using `dput(head(df,20))` or some kind of dummy data to work with? — NelsonGon, Jan 09 '19 at 17:43
That's a tricky one! I found it in one of the answers on stack overflow: https://stackoverflow.com/questions/35717353/split-violin-plot-with-ggplot2. If it becomes tricky like that, I'd also be happy to change the colors of the boxplots or already the outline of the boxplots! — Marretje Adriaanse, Jan 09 '19 at 18:08

conv3d · Accepted Answer · 2019-01-09T18:46:21.760

You can add an additional column to your data that is the same structure as TM but different values, then scale the fill:

Sample Data:

data <- data.frame(TM = c(rep("org", 5), rep("min", 5),rep("org", 5), rep("min", 5),rep("org", 5), rep("min", 5)),
                 Zscore = runif(30,-2,2),
                 X = c(rep("zwfa", 10), rep("zhfa", 10), rep("zbfa", 10)))

Begin solution:

data <- data %>% mutate(TMm = c(rep("orgM", 5), rep("minM", 5),rep("orgM", 5), rep("minM", 5),rep("orgM", 5), rep("minM", 5)))
#Colours
ocean = c('#BBDED6' , '#FAE3D9', '#61C0BF'  , '#FFFFFF')

## Plot ##
z <- ggplot(data = data, aes(x = X, y = Zscore,fill=TM)) +
  geom_split_violin(mapping = aes(fill=TMm))  +
  geom_boxplot(alpha = 1, width=0.3, aes(fill=TM), position = position_dodge(width = 0.3))          

z + theme(axis.text = element_text(size = 12),legend.position="top")  +
  stat_compare_means(method="t.test", label.y=2.8, label.x=0.3, size=3) +
  scale_fill_manual(breaks = c("org", "min"), values=ocean, labels=c("Mineral fertilizer", "Organic fertilizer"))

In your data you may have to change breaks = c("org", "min") to whatever you call the factor levels in the TM variable

Or if you want the whole violin plot white:

ocean = c('#BBDED6' , '#FFFFFF', '#61C0BF' , '#FFFFFF')

New Plot:

I have on more problem though, I am not sure if it happening with your try as well (it looks like it): but for the zhfa (the second one), the violin plot gets turned around. Zo the boxplot of the left lighter coloured 'treatment', does not fit with the violin plot on the left. When I change the geom_split_violin to geom_violin it becomes extra clear that they get switched around while the violin plots of the zbfa and zwfa are on the correct place. I am guessing this is a problem with the geom_split_violin function. — Marretje Adriaanse, Jan 11 '19 at 14:48

How to get different colors related to treatment for boxplot and violin plot (ggplot / using geom_split_violin) that are plotted in one?

1 Answers1