misaligned bars in geom_bar using fill

Question

I have a problem with ggplot's geom_bar.

I have several bar charts rendered from several variables all using the same fourth variable as a fill:

For some reason in the third chart the columns for cohort 2 are misaligned. All three charts use the same Dataset and the same code.

library(tidyverse)
library(patchwork)
myColours <- c("#A71C49","#11897A","#DD4814", "#282A36")


DataSet <- structure(list(`Var1` = c(3, 2, 5, 3, 4, 1, 3, 1, 
                                     5, 4, 5, 3, 5, 5, 5, 4, 4, 5, 4, 5, 5, 5, 5, 1, 5, 5, 4, 4, 3, 
                                     5, 5, 4, 1, 3, 5, 2, 5, 5, 4, 4, 2, 5, 1, 5, 3, 5, 5, 5, 2, 5, 
                                     3, 1, 5, 5, 5, 5, 4), `Var2` = c(3, 1, 4, 1, 2, 2, 
                                                                      3, 1, 3, 3, 3, 3, 2, 5, 5, 1, 4, 4, 5, 5, 4, 5, 3, 2, 3, 5, 2, 
                                                                      3, 3, 5, 5, 2, 1, 3, 4, 2, 4, 5, 3, 3, 5, 3, 1, 4, 3, 5, 3, 4, 
                                                                      2, 4, 1, 4, 4, 5, 1, 3, 3), `Var3` = c(3, 2, 1, 
                                                                                                             3, 1, 4, 3, 2, 4, 3, 3, 3, 5, 3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 4, 
                                                                                                             5, 2, 4, 4, 4, 5, 5, 1, 1, 3, 5, 2, 5, 5, 3, 4, 3, 1, 1, 4, 3, 
                                                                                                             2, 5, 4, 2, 4, 4, 1, 4, 5, 1, 5, 2), Cohort = structure(c(1L, 
                                                                                                                                                                       1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 
                                                                                                                                                                       3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
                                                                                                                                                                       3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 
                                                                                                                                                                       4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("1", "2", "3", "4"
                                                                                                                                                                       ), class = "factor")), row.names = c(NA, -57L), class = c("tbl_df", 
                                                                                                                                                                                                                                 "tbl", "data.frame"))


c5 <- ggplot(DataSet, aes(`Var1`, fill=Cohort)) +
  geom_bar() +
  theme(legend.position = "none")  +
  ylim(0,25) +
  scale_fill_manual(values=myColours)

c6 <- ggplot(DataSet, aes(`Var2`, fill=Cohort)) +
  geom_bar() +
  theme(legend.position = "none")  +
  ylim(0,25) +
  scale_fill_manual(values=myColours)

c7 <- ggplot(DataSet, aes(`Var3`, fill=Cohort)) +
  geom_bar() +
  ylim(0,25) +
  scale_fill_manual(values=myColours)

(c5 | c6 ) /
(c7 | guide_area())

I have the following error messages:

1: Removed 2 rows containing missing values (geom_bar). 
2: position_stack requires non-overlapping x intervals 

The missing values refer to the graph for Var1, the non-overlapping x intervals for the third graph. If I render out just Cohort two I also get these weirdly misaligned bars:

And Cohort 3 Var 3 to compare

I would have suspected the fact, that there are only two different numbers in cohort 2, but it works for the barchart with Var1 above. It is also not patchwork buggering it up, as it is the same when I render out just the Var3 barchart. It is also not the legend only being rendered for the Var3 Graph

Does anyone have an idea what the problem is or how I can force ggplot to align the bars correctly?

Thank you!

(R version 4.0.4 Patched (2021-02-17 r80030); tidyverse v.1.3.1; patchwork v.1.1.1)

Answer 1

The third graph is misaligned as stacked barplots interpret the value as numerical, making it unsuitable for stacking (do you stack x=1 and x= 1.00001 on top of each other etc.?). Transforming it to an ordered vector helps ggplot understand.

Consider this example only using the tidyverse:

myColours <- c("#A71C49","#11897A","#DD4814", "#282A36")

# Lenthen the dataset
DataSet2 <- DataSet %>% pivot_longer(cols = -Cohort,names_to = "Variable")

# This helps against the non-overlapping x intervals issue
DataSet2$value <- as.ordered(DataSet2$value)

ggplot(DataSet2,aes(x=value,fill=Cohort)) +
  geom_bar(position= position_stack()) + ylim(0,25)+
  facet_wrap(vars(Variable)) +  # make multiple graphs split by the column "Variable"
  scale_fill_manual(values=myColours)

Result: