Reordering boxplot (ggplot) with scale_x_discrete(limits=(...) results in Warning message: Removed 103 rows containing missing values (stat_boxplot)

Question

Probably a user error but I can't find it for the life of me. Trying to rearrange the order of factors in a boxplot I am making using ggplot using the, "scale_x_discrete(limits=(...)" function. Doing so results in the following warning message "Warning message: Removed 103 rows containing missing values (stat_boxplot". and a plot where one grouping is missing it's boxplot all together. I am confused as this has worked just fine for nearly identical plots of other factors, and the plot is totally normal if I don't try to rearrange and run it as is. There is nothing wrong with the underlying dataframe that I can tell (e.g. no missing values or NAs). Any thoughts on what the issue might be here?

Thanks!

example of boxplot pre-issue:

maxn_topo_plot<- ggplot(wide.df2, aes(x=topo, y=sum_maxn)) + 
  geom_boxplot(show.legend = FALSE) + theme_pubclean(base_size = 20) +  xlab("Island Geomorpholgy") + ylab("Shark MaxN") + 
 theme(axis.text.x =  element_text(angle = 12))


maxn_topo_plot

The code that has the issue:

maxn_topo_plot<- ggplot(wide.df2, aes(x=topo, y=sum_maxn)) + 
  geom_boxplot(show.legend = FALSE) + theme_pubclean(base_size = 20) +  xlab("Island Geomorpholgy") + ylab("Shark MaxN") + 
  scale_x_discrete(limits=c("open atoll","closed atoll","near atoll", "high barrier", "high rocky", "high fringing")) + 
  theme(axis.text.x =  element_text(angle = 12))


maxn_topo_plot

code that works just fine:

max_isl_group<- ggplot(wide.df2, aes(x=isl_grp, y=sum_maxn)) + 
geom_boxplot(show.legend = FALSE) + theme_pubclean(base_size = 20) +  xlab("Island Group") + ylab("Shark MaxN") + 
 scale_x_discrete(limits=c("west tuamotu","east tuamotu","windward", "leeward", "marquesas", "australes")) + 
  theme(axis.text.x =  element_text(angle = 20))

max_isl_group 

Answer 1

I dont know exactly whats happening on your code

But, if you want other way to reorder the x axis without this message here it is:

maxn_topo_plot<- ggplot(wide.df2, aes(x= factor(topo,
                                          levels = c("open atoll",
                                                     "closed atoll",
                                                     "near atoll", 
                                                     "high barrier", 
                                                     "high rocky", 
                                                     "high fringing")), y=sum_maxn)) + 
  geom_boxplot(show.legend = FALSE)  +  
  xlab("Island Geomorpholgy") + 
  ylab("Shark MaxN") + 
  theme_pubclean(base_size = 20) +
  theme(axis.text.x =  element_text(angle = 12))

Answer 2

It was a rogue space in one of my factors "high fringing" that was the underlying issue. bangs head on desk. Hours well spent.