Adding trend lines across groups and setting tick labels in a grouped violin plot or box plot

Question

I have xy grouped data that I'm plotting using R's ggplot2 geom_violin adding regression trend lines:

Here are the data:

library(dplyr)
library(plotly)
library(ggplot2)

set.seed(1)
df <- data.frame(value = c(rnorm(500,8,1),rnorm(600,6,1.5),rnorm(400,4,0.5),rnorm(500,2,2),rnorm(400,4,1),rnorm(600,7,0.5),rnorm(500,3,1),rnorm(500,3,1),rnorm(500,3,1)),
                 age = c(rep("d3",500),rep("d8",600),rep("d24",400),rep("d3",500),rep("d8",400),rep("d24",600),rep("d3",500),rep("d8",500),rep("d24",500)),
                 group = c(rep("A",1500),rep("B",1500),rep("C",1500))) %>%
  dplyr::mutate(time = as.integer(age)) %>%
  dplyr::arrange(group,time) %>%
  dplyr::mutate(group_age=paste0(group,"_",age))

df$group_age <- factor(df$group_age,levels=unique(df$group_age))

And my current plot:

ggplot(df,aes(x=group_age,y=value,fill=age,color=age,alpha=0.5)) + 
  geom_violin() + geom_boxplot(width=0.1,aes(fill=age,color=age,middle=mean(value))) + 
  geom_smooth(data=df,mapping=aes(x=group_age,y=value,group=group),color="black",method='lm',size=1,se=T) + theme_minimal()

My questions are:

1. How do I get rid of the alpha part of the legend?
2. I would like the x-axis ticks to be df$group rather than df$group_age, which means a tick per each group at the center of that group where the label is group. Consider a situation where not all groups have all ages - for example, if a certain group has only two of the ages and I'm pretty sure ggplot will only present only these two ages, I'd like the tick to still be centered between their two ages.

One more question:

It would also be nice to have the p-values of each fitted slope plotted on top of each group.

I tried:

library(ggpmisc)
my.formula <- value ~ group_age
ggplot(df,aes(x=group_age,y=value,fill=age,color=age,alpha=0.5)) + 
  geom_violin() + geom_boxplot(width=0.1,aes(fill=age,color=age,middle=mean(value))) + 
  geom_smooth(data=df,mapping=aes(x=group_age,y=value,group=group),color="black",method='lm',size=1,se=T) + theme_minimal() +
  stat_poly_eq(formula = my.formula,aes(label=stat(p.value.label)),parse=T)

But I get the same plot as above with the following warning message:

Warning message:
Computation failed in `stat_poly_eq()`:
argument "x" is missing, with no default 

Answer 1

geom_smooth() fits a line, while stat_poly_eqn() issues an error. A factor is a categorical variable with unordered levels. A trend against a factor is undefined. geom_smooth() may be taking the levels and converting them to "arbitrary" numerical values, but these values are just indexes rather than meaningful values.

To obtain a plot similar to what is described in the question but using code that provides correct linear regression lines and the corresponding p-values I would use the code below. The main change is that the numerical variable time is mapped to x making the fitting of a regression a valid operation. To allow for a linear fit an x-scale with a log10 transformation is used, with breaks and labels at the ages for which data is available.

library(dplyr)
library(ggplot2)
library(ggpmisc)

set.seed(1)
df <-
  data.frame(
    value = c(
      rnorm(500, 8, 1), rnorm(600, 6, 1.5), rnorm(400, 4, 0.5),
      rnorm(500, 2, 2), rnorm(400, 4, 1), rnorm(600, 7, 0.5),
      rnorm(500, 3, 1), rnorm(500, 3, 1), rnorm(500, 3, 1)
    ),
    age = c(
      rep("d3", 500), rep("d8", 600), rep("d24", 400),
      rep("d3", 500), rep("d8", 400), rep("d24", 600),
      rep("d3", 500), rep("d8", 500), rep("d24", 500)
    ),
    group = c(rep("A", 1500), rep("B", 1500), rep("C", 1500))
  ) %>%
  mutate(time = as.integer(gsub("d", "", age))) %>%
  arrange(group, time) %>%
  mutate(age = factor(age, levels = c("d3", "d8", "d24")),
         group = factor(group))

my_formula = y ~ x

ggplot(df, aes(x = time, y = value)) +
  geom_violin(aes(fill = age, color = age), alpha = 0.3) + 
  geom_boxplot(width = 0.1,
               aes(color = age), fill = NA) +
  geom_smooth(color = "black", formula = my_formula, method = 'lm') + 
  stat_poly_eq(aes(label = stat(p.value.label)), 
               formula = my_formula, parse = TRUE,
               npcx = "center", npcy = "bottom") +
  scale_x_log10(name = "Age", breaks = c(3, 8, 24)) +
  facet_wrap(~group) +
  theme_minimal()

Which creates the following figure:

Answer 2

Here is a solution. The alpha - legend issue is easy. Anything you place into the aes() functioning will get placed in a legend. This feature should be used when you want a feature of the data to be used as an aestetic. Putting alpha outside of an aes will remove it from the legend.

I'm not sure the x legend is what you wanted but i did it manually so it should be easy to configure.

Regarding the p.values, i did separate linear regressions and store the p.value in three different vectors which can be called into the ggplot using the annotate. For two of the groups the p.value was <.001 so the round functioning will round it to 0. Therefore, i just added p. <.001

Good luck with this!

library(dplyr)
library(ggplot2)

set.seed(1)
df <- data.frame(value = c(rnorm(500,8,1),rnorm(600,6,1.5),rnorm(400,4,0.5),rnorm(500,2,2),rnorm(400,4,1),rnorm(600,7,0.5),rnorm(500,3,1),rnorm(500,3,1),rnorm(500,3,1)),
                 age = c(rep("d3",500),rep("d8",600),rep("d24",400),rep("d3",500),rep("d8",400),rep("d24",600),rep("d3",500),rep("d8",500),rep("d24",500)),
                 group = c(rep("A",1500),rep("B",1500),rep("C",1500))) %>%
  dplyr::mutate(time = as.integer(age)) %>%
  dplyr::arrange(group,time) %>%
  dplyr::mutate(group_age=paste0(group,"_",age))

df$group_age <- factor(df$group_age,levels=unique(df$group_age))

mod1 <- lm(value ~ time,df\[df$group == 'A',\])
mod1 <- summary(mod1)$coefficients\[8\] %>% round(2)

mod2 <- lm(value ~ time,df\[df$group == 'B',\])
mod2 <- summary(mod2)$coefficients\[8\] %>% round(2)

mod3 <- lm(value ~ time,df\[df$group == 'C',\])
mod3 <- summary(mod3)$coefficients\[8\] %>% round(2)



ggplot(df,aes(x=group_age,y=value,fill=age,color=age)) + 
  geom_violin(alpha=0.5) + 
  geom_boxplot(width=0.1,aes(fill=age,color=age,middle=mean(value))) + 
  geom_smooth(mapping=aes(x=group_age,y=value,group=group),color="black",method='lm',size=1,se=T) + 
  scale_x_discrete(labels = c('','A','','','B','','','C','')) +
  annotate('text',x = 2,y = -1,label = paste('pvalue: <.001')) +
  annotate('text',x = 6,y = 10,label = paste('pvalue: <.001')) +
  annotate('text',x = 8,y = -1.2,label = paste('pvalue:',mod3))+
  theme_minimal()