Re: [R] How to add error bars to a line plot with ggplot2?

Fri, 14 Jul 2023 10:06:22 -0700 

Às 17:33 de 14/07/2023, Luigi Marongiu escreveu:

Hello,
I am measuring a certain variable at given time intervals and
different concentrations of a reagent. I would like to make a scatter
plot of the values, joined by a line to highlight the temporal
measure.
I can plot this all right. Now, since I have more than one replicate,
I would like to add he error bars.
I prepared  a dataframe with the mean measures and a column with the
standard deviations, but when I run the code, I get the error:
```
Error in `check_aesthetics()`:
! Aesthetics must be either length 1 or the same as the data (20): colour
Run `rlang::last_trace()` to see where the error occurred.
```
I am missing something, but what?
Thank you


WORKING EXAMPLE
```
measTime    = c(1    ,2    ,4    ,24    ,48    ,1    ,2    ,4    ,24
  ,48    ,1    ,2    ,4    ,24    ,48    ,1    ,2    ,4    ,24    ,48)
conc    = c(0.25    ,0.25    ,0.25    ,0.25    ,0.25    ,1.12    ,1.12
    ,1.12    ,1.12    ,1.12    ,2.5    ,2.5    ,2.5    ,2.5    ,2.5
,25    ,25    ,25    ,25    ,25)
varbl    = c(0.0329999999999999    ,0.27    ,0.0785    ,0.1015
,-0.193    ,0.048    ,0.113    ,0.1695    ,-0.775    ,0.464    ,-0.257
    ,-0.154    ,-0.3835    ,-1.23    ,-0.513    ,1.3465    ,1.276
,1.128    ,-2.56    ,-1.813)
stdDev    =c(0.646632301492381    ,0    ,1.77997087991162
,0.247683265482349    ,0    ,0.282901631902917    ,0
,0.273086677326693    ,1.03807578400295    ,0    ,0.912213425319609
,0    ,1.64371621638287    ,2.23203614068709    ,0    ,0.2615396719429
    ,0    ,0.54039985196149    ,2.15236180353893    ,0)
df = data.frame(Time=measTime, mM=conc, ddC=varbl, SD=stdDev)
library(ggplot2)
COLS = c("green", "red", "blue", "yellow")
   ggplot(df,
          aes(x=Time, y=ddC, colour=mM, group=mM)) +
   geom_line(aes(x=Time, y=ddC, colour=mM, group=mM)) +
   geom_errorbar(aes(x=Time, ymin=ddC-SD, ymax=ddC+SD, colour=mM, group=mM),
                 width=.1, colour=COLS) +
   geom_point(size=6) +
   scale_colour_manual(values = COLS) +
   ggtitle("Exposure") +
   xlab(expression(bold("Time (h)"))) +
   ylab(expression(bold("Value"))) +
   geom_hline(aes(yintercept=0)) +
   theme_classic()
   ```

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Hello,

Two notes:
1. If you want to use a discrete colours vector, your 'colour' aesthetic must be mapped to a discrete variabe. The most frequent cases are character or factor columns.
2. If you start the plot with certain aesthetics set you don't have to repeat them in subsequent layers, geom_line can be called with no aes() and gem_errorbar doesn't need x=measTime again.
As for the main error, the colors vector COLS should be removed from geom_errorbar. 



df <- data.frame(Time = measTime,
                 mM = factor(conc),  # this must be a factor
                 ddC = varbl,
                 SD = stdDev)

library(ggplot2)

COLS = c("green", "red", "blue", "yellow")

ggplot(df, aes(x = Time, y = ddC, colour = mM, group = mM)) +
  geom_line() +
  geom_errorbar(aes(ymin = ddC - SD, ymax = ddC + SD), width = 0.1) +
  geom_point(size = 6) +
  geom_hline(aes(yintercept = 0)) +
  scale_colour_manual(values = COLS) +
  ggtitle("Exposure") +
  xlab(expression(bold("Time (h)"))) +
  ylab(expression(bold("Value"))) +
  theme_classic()


Hope this helps,

Rui Barradas

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