Why are my Y values much higher than 100% even though my highest value is 63%

Question

I'm trying to plot a graph using ggplot2 builder. My graph has species (Sp.) for X and percentage (Cover) for Y, with Gradient as groups and Sites as facet. However, my graph is giving me a value of 400 on the Y axis.

This is my df structure:

> data.frame':  720 obs. of  6 variables:
> Site    : Factor w/ 2 levels "DRP","PSP": 2 2 2 2 2 2 2 2 2 2 ...
> Plot_ID : int  1 2 3 4 5 6 7 8 9 10 ...
> Gradient: Factor w/ 3 levels "Low","Medium",..: 3 3 3 3 3 3 3 3 3 3 ...
> Sp.     : Factor w/ 4 levels "AG","FA","SN",..: 2 2 2 2 2 2 2 2 2 2 ...
> P.A     : int  1 1 1 1 1 1 1 1 1 1 ...
> Cover   : int  16 36 16 36 36 63 16 36 36 36 ...

This is my df table:

Site Plot_ID Gradient Sp. P.A Cover G2 Percentage
> 1  PSP       1     High  FA   1    16  3       0.16
> 2  PSP       2     High  FA   1    36  3       0.36
> 3  PSP       3     High  FA   1    16  3       0.16
> 4  PSP       4     High  FA   1    36  3       0.36
> 5  PSP       5     High  FA   1    36  3       0.36
> 6  PSP       6     High  FA   1    63  3       0.63

Sample of dataset:

Site    Plot_ID Gradient    Sp. P/A Cover
PSP 1   High    FA  1   16
DRP 1   Medium  FA  0   0
PSP 1   High    AG  1   16
DRP 1   Medium  AG  0   0
PSP 1   High    SS  0   0
DRP 1   Medium  SS  0   0
PSP 1   High    SN  1   16
DRP 1   Medium  SN  0   0
PSP 2   High    FA  1   36
DRP 2   Medium  FA  0   0
PSP 2   High    AG  0   0
DRP 2   Medium  AG  1   3
PSP 2   High    SS  0   0
DRP 2   Medium  SS  0   0
PSP 2   High    SN  0   0
DRP 2   Medium  SN  0   0
PSP 3   High    FA  1   16
DRP 3   High    FA  1   1
PSP 3   High    AG  1   16
DRP 3   High    AG  1   36
PSP 3   High    SS  0   0
DRP 3   High    SS  0   0
PSP 3   High    SN  0   0
DRP 3   High    SN  0   0
PSP 4   High    FA  1   36
DRP 4   High    FA  1   16
PSP 4   High    AG  0   0
DRP 4   High    AG  1   1
PSP 4   High    SS  0   0
DRP 4   High    SS  1   16
PSP 4   High    SN  0   0
DRP 4   High    SN  1   16
PSP 5   High    FA  1   36
DRP 5   Medium  FA  0   0
PSP 5   High    AG  0   0
DRP 5   Medium  AG  0   0
PSP 5   High    SS  0   0
DRP 5   Medium  SS  0   0
PSP 5   High    SN  0   0

This is the code ggplot gave me:

ggplot(df) +
  aes(
    x = Sp.,
    fill = Gradient,
    group = Gradient,
    weight = Cover
  ) +
  geom_bar(position = "dodge") +
  scale_fill_brewer(palette = "Greys", direction = 1) +
  theme_bw() +
  facet_wrap(vars(Site))

This is the result graph. As you can see Y axis is showing 400, but my highest % cover is 63%.

It doesn't make sense to me to have 400 for Y. As can be seen in the table header I try to divide the % cover by 100 (as was suggested in a different post), but the only thing that changed was that instead of 400 the Y axis higher level was 4.

I'd also like to have error bars in the graph.

Answer 1

I think you want something like this, where you are plotting the mean +- CI for each category.

ggplot(df, aes(Sp., Cover, fill = factor(Gradient))) + 
  stat_summary(fun = mean, geom = 'bar', position = 'dodge') + 
  stat_summary(
    fun.data = 'mean_cl_boot', geom = 'errorbar', 
    position = position_dodge(width = 0.9), width = 0.2
  )