How to add data points in ggplot curve?

Question

I am plotting a curve using ggplot. I have the data which I calculated mean and se and stored in data. Then I used ggplot to plot the curve. So far everything looks good. But, I would like to scatter all three replicate data points for each time point and dose over their respective mean error bar. Can anyone help with my query. Here is my code:

structure(list(values = c(5L, 3L, 2L, 6L, 4L, 1L, 5L, 3L, 1L, 
25L, 15L, 10L, 30L, 17L, 9L, 27L, 14L, 8L, 75L, 45L, 20L, 80L, 
50L, 25L, 90L, 50L, 30L, 150L, 100L, 50L, 160L, 110L, 60L, 170L, 
120L, 70L), dose = structure(c(3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 
1L, 3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 
3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L, 3L, 2L, 1L), .Label = c("2.5", 
"5", "10"), class = "factor"), time = c(0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 20L, 
20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 30L, 30L, 30L, 30L, 30L, 
30L, 30L, 30L, 30L)), row.names = c(NA, -36L), class = "data.frame")


my_data$dose <- as.factor(my_data$dose)
head(my_data)

library(dplyr)
data <- group_by(my_data, dose, time) %>%
 summarise(
  count = n(),
  mean = mean(values, na.rm = TRUE),
  sd = sd(values, na.rm = TRUE),
  se   = sd / sqrt(n())
  )

data

p <- ggplot(data, aes(x=time, y=mean, group=dose)) +
 geom_point(size = 1)+
 geom_smooth(aes(linetype=dose), color = "black", se = F, size = 0.5)+
 geom_errorbar(aes(ymin=mean - se, ymax=mean + se), width=1.8) + 
 labs(x ="sec", y = "Units") +
 scale_x_continuous(breaks = seq(0, 35, 5), limits = c(-1, 35), expand = c(0, 0))+
 scale_y_continuous(breaks = seq(0, 200, 20), limits = c(-10, 200), expand = c(0, 0))+
 scale_linetype_manual(values=c( "dashed",  "dotted", "solid"),
                        labels = c("2.5", "5", "10"))
p

Rui Barradas · Accepted Answer · 2020-01-13 06:28:29Z

3

The points to be plotted are present in the original data set my_data but not in the aggregated data. In the latter only the mean values are present. So argument data = my_data must be passed to geom_point.

p <- ggplot(data, aes(x = time, y = mean, group = dose)) +
  geom_point(data = my_data, 
             mapping = aes(x = time, y = values), 
             size = 1) +
  geom_smooth(data = data, 
              mapping = aes(linetype = dose), 
              color = "black", 
              se = FALSE, size = 0.5)+
  geom_errorbar(aes(ymin = mean - se, ymax = mean + se), width=1.8) + 
  labs(x ="sec", y = "Units") +
  scale_x_continuous(breaks = seq(0, 35, 5), 
                     limits = c(-1, 35), expand = c(0, 0)) +
  scale_y_continuous(breaks = seq(0, 200, 20), 
                     limits = c(-10, 200), expand = c(0, 0)) +
  scale_linetype_manual(values = c( "dashed",  "dotted", "solid"),
                        labels = c("2.5", "5", "10"))

p

answered Jan 13, 2020 at 6:28

Rui Barradas

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2 Comments

user12582271 Over a year ago

Thank you so much. This is really helpful. I am wondering if I can show additionally mean_se error bar (i.e. some dot (mean) in the middle of upper and lower whiskers). Is this possible?

Rui Barradas Over a year ago

@user12582271 Yes, it is possible. Use the same trick, in geom_point pass the appropriate data set to argument data and set the aes to the values you want to plot.

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