Plot boxplots over time using multiple categories - r

Question

I am sorry for the header I was not so sure how to ask about it.
I have a data frame that looks like this.
Sample=c("A","A", "A", "B","B","B","A","A", "A", "B","B","B","A","A", "A", "B","B","B","A","A", "A", "B","B","B")
Treatment=c("twiter","twiter","twiter","twiter","twiter","twiter","facebook","facebook","facebook","facebook","facebook","facebook",
"twiter","twiter","twiter","twiter","twiter","twiter","facebook","facebook","facebook","facebook","facebook","facebook")
replicate=c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3)
time=c( 10,10,10,10,10,10,10,10,10,10,10,10,20,20,20,20,20,20,20,20,20,20,20,20)
points=c(20,40,80,20,60,120, 30,100,55, 28, 45,90, 80,20,100, 40,90,56,20,30,12,3,5,8)
length(points)
Sample Treatment replicate time points
1 A twiter 1 10 20
2 A twiter 2 10 40
3 A twiter 3 10 80
4 B twiter 1 10 20
5 B twiter 2 10 60
6 B twiter 3 10 120
7 A facebook 1 10 30
8 A facebook 2 10 100
9 A facebook 3 10 55
10 B facebook 1 10 28
11 B facebook 2 10 45
12 B facebook 3 10 90
13 A twiter 1 20 80
14 A twiter 2 20 20
15 A twiter 3 20 100
16 B twiter 1 20 40
17 B twiter 2 20 90
18 B twiter 3 20 56
19 A facebook 1 20 20
20 A facebook 2 20 30
21 A facebook 3 20 12
22 B facebook 1 20 3
23 B facebook 2 20 5
24 B facebook 3 20 8
I would like to plot my data using boxplots at each time point.
I would like to have one box plot that shows Sample A with "twiter" Sample A with "facebook"
Sample "B" with "twiter" and Sample B with "facebook" at time point 10 and the same at time point 20.
So far I can do something like this.
ggplot(data,aes(x=time, y=points,color=Sample, fill=Sample, group=interaction(Sample,Treatment)), alpha=0.1) +
geom_boxplot(alpha=0.1) +
geom_point(position = position_dodge(width=0.75), alpha=0.2)+
theme_bw()
But this is wrong I would like to have the sample A, and B from the two different treatments next to each other at each time point to have a look at the differences. I don't want to use facet_wrap. It is a challenge for me. Thank you for your time

Answer 1

Turning my comment into an answer: your issue is that group=interaction(Sample,Treatment) overrides the grouping by the x-axis (time) that would normally be done. To include time in the grouping, add it to the interaction:
ggplot(data,
aes(
x = time,
y = points,
color = Sample,
fill = Sample,
group = interaction(Sample, Treatment, time)
),
alpha = 0.1) +
geom_boxplot(alpha = 0.1) +
geom_point(position = position_dodge(width = 0.75), alpha = 0.2) +
theme_bw()
Of course, the issue remains that there's no way to tell which box goes with which treatment, but I'll leave that to you to address.

Answer 2

Try this:
library(dplyr)
library(ggplot2)
#Plot
data %>%
arrange(Sample) %>%
mutate(Var=paste(Sample,Treatment),
Var=factor(Var,levels = unique(Var),ordered = T)) %>%
ggplot(aes(x=time,
y=points,
color=Var, fill=Var,
group=Var), alpha=0.1) +
geom_boxplot(alpha=0.1)+
geom_point(position = position_dodge(width=0.75), alpha=0.2)+
theme_bw()+
scale_color_manual(values=c('tomato','tomato','cyan3','cyan3'))+
scale_fill_manual(values=c('tomato','tomato','cyan3','cyan3'))
Output:

Answer 3

If you don't mind making time a factor, you can do the following. Note that I turned your data into a data frame named 'dat'.
dat <- data.frame(Sample=c("A","A", "A", "B","B","B","A","A", "A", "B","B","B","A","A", "A", "B","B","B","A","A", "A", "B","B","B"),
Treatment=c("twiter","twiter","twiter","twiter","twiter","twiter","facebook","facebook","facebook","facebook","facebook","facebook",
"twiter","twiter","twiter","twiter","twiter","twiter","facebook","facebook","facebook","facebook","facebook","facebook"),
replicate=c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3),
time=c( 10,10,10,10,10,10,10,10,10,10,10,10,20,20,20,20,20,20,20,20,20,20,20,20),
points=c(20,40,80,20,60,120, 30,100,55, 28, 45,90, 80,20,100, 40,90,56,20,30,12,3,5,8))
dat %>%
mutate(time = factor(time)) %>%
ggplot(aes(x=time, y=points, color=Sample, fill=Sample), alpha=0.1) +
geom_boxplot(alpha=0.1) +
geom_point(position = position_dodge(width=0.75), alpha=0.2)+
theme_bw()