ggplot : Adding mean/error bars for dotplot with different groups - r

Question

I'm new to ggplot and starting from this graph :
library(ggplot2)
library(reshape2)
data <- read.delim(textConnection("
Sample Day_0 Day_1 Day_4 Day_5 Day_7
NM 1000 221000 6620000 17200000 43700000
OG 1000 351000 1750000 6880000 18300000
OD 1000 961000 1090000 6380000 4400000
ODD 1000 1060000 3550000 12000000 13100000"), sep = " ")
data_melt <- melt(data, id.var = "Sample")
data_melt$value <- as.numeric(data_melt$value)
ggplot(data=data_melt, aes(x=variable, y=value, color = Sample)) + geom_point(size = 2.5) + scale_y_continuous(trans=log2_trans(), breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x))) +
ggtitle("My_Title") + xlab("My_X") + ylab("My_Axis") + theme(plot.title = element_text(hjust = 0.5)) + expand_limits(y = c(10^3, 10^8))
see the graph result
What I would like to do is to add mean and error bars of the 4 points each of the "Days" (in this kind of way for example, picture from http://www.sthda.com/).
Any method/advice would be helpful !

Answer 1

You could do this using geom_errorbarand adding the relevant statistics when defining your data set. For the length of the error bars the code below simply uses the the 0.25/0.75 empirical quantiles. If you want to change that, just change lower and upper to the ranges you are interested in.
library(dplyr)
data_melt <- data_melt %>% group_by(variable) %>% mutate(upper = quantile(value, 0.75),
lower = quantile(value, 0.25),
mean = mean(value))
# How the first 9 values of your data set should look like now:
#A tibble: 20 x 6
## Groups: variable [5]
#Sample variable value upper lower mean
#<fctr> <fctr> <dbl> <dbl> <dbl> <dbl>
#1 NM Day_0 1000 1000 1000 1000
#2 OG Day_0 1000 1000 1000 1000
#3 OD Day_0 1000 1000 1000 1000
#4 ODD Day_0 1000 1000 1000 1000
#5 NM Day_1 221000 985750 318500 648250
#6 OG Day_1 351000 985750 318500 648250
#7 OD Day_1 961000 985750 318500 648250
#8 ODD Day_1 1060000 985750 318500 648250
#9 NM Day_4 6620000 4317500 1585000 3252500
ggplot(data=data_melt, aes(x=variable, y=value, color = Sample)) +
geom_point(size = 2.5) + scale_y_continuous(trans=log2_trans(),
breaks = trans_breaks("log10",
function(x) 10^x),
labels = trans_format("log10",
math_format(10^.x))) +
ggtitle("My_Title") +
xlab("My_X") + ylab("My_Axis") +
theme(plot.title = element_text(hjust = 0.5)) +
expand_limits(y = c(10^3, 10^8)) +
geom_errorbar(aes(ymin = lower, ymax = upper),col = "red",
width = 0.25) +
geom_point(aes(x = variable, y = mean), size = 3, col = "red")