I am trying to use tidyverse
more and and pivot_longer
to later plot error bars over geom_errorbar
(one dashed and one solid), but I believe I am not building the long format right or somehow the error_bars aren't well connected with the function.
data<- data.frame(
Date=(1:12),
A=c(0,0,0,28.0,20.6,15.8,38.9,9.5,16.2,20.6,22.6,15.1),
B= c(0,0,0,9.1,6.0,4.76,12.7,4.3,5.7,8.0,9.01,6.5),
A_sd= c(0,0,0,6.3,11.4,1.49,6.96,1.23,1.4,1.15,6.3,1.2),
B_sd=c(0,0,0,1.90,3.1,0.24,1.8,1.16,0.4,1.4,2.4,0.5))
LINETYPE1 <- c("A" = "solid", "B" = "dashed")
library(tidyverse)
data %>%
select(A, B, A_sd, B_sd, Date) %>%
pivot_longer(cols = -Date, -A_sd, -B_sd) %>%
ggplot(aes(Date, value, linetype = name))
geom_line()
geom_point()
scale_y_continuous(sec.axis = sec_axis(~./10, name= expression(paste("B", " (units)"))))
scale_linetype_manual(name= "", values= LINETYPE1, labels=c(bquote(A ~ (pg ~cell ^-1)), bquote(B ~ (units))))
scale_x_datetime(labels = date_format("%b"))
theme_classic()
ylab(bquote(A ~ (units)))
geom_errorbar(aes(ymin = A, ymax = A A_sd),
position = position_dodge2(padding = 0.6, width = 0.5))
geom_errorbar(aes(ymin = B, ymax = B B_sd),
position = position_dodge2(padding = 0.6, width = 0.5))
xlab("")
This now gives the error:
Error in build_longer_spec(data, !!cols, names_to = names_to, values_to = values_to, : object 'B_sd' not found
I would love to get something like this
CodePudding user response:
Yes, your pivot wasn't quite right. The easiest way to do it from your sample data is to first rename A
and B
as something like A_mean
and B_mean
, then use the names_sep
method in pivot_longer
. That way, you can call:
pivot_longer(-Date, names_sep = "_", names_to = c("group", ".value"))
To leave you with one column each for Date, group (A/B), mean and sd.
The complete code would be something like this:
data %>%
select(A, B, A_sd, B_sd, Date) %>%
rename(A_mean = A, B_mean = B) %>%
pivot_longer(-Date, names_sep = "_", names_to = c("group", ".value")) %>%
ggplot(aes(Date, mean, linetype = group))
geom_line()
geom_point()
scale_y_continuous(sec.axis = sec_axis(~./10,
name= expression(paste("B", " (units)"))))
scale_linetype_manual(name= "", values = LINETYPE1,
labels=c(bquote(A ~ (pg ~cell ^-1)),
bquote(B ~ (units))))
scale_x_datetime(labels = scales::date_format("%b"))
theme_classic(base_size = 16)
ylab(bquote(A ~ (units)))
geom_errorbar(aes(ymin = mean -sd, ymax = mean sd), alpha = 0.5)
xlab("")
Note that I had to modify your input data slightly to change the Date
column to actual dates, otherwise your scale_x_datetime
call doesn't work.